[6]

[7]

[8]

[9]

[10]

Contract Beamlines

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[13]

"Ǿ Meson Production Experiments at SPring-8"
M. Fujiwara
Heavy Ion Physics, 12, (2000), 131-141"Experiment at SPring-8"
T. Nakano, J. Ahn, H. Ejiri, M. Fujiwara, T. Hotta, N. Matsuoka, T. Matsumura, T. Mibe, M. Nomachi,
H. Toki, C. Wang, S. Wang, H. Kawai, T. Ooba, T. Iwata, Y. Miyachi, T. Toyama, A. Wakai, K. Hicks,
H. Akimune, Y. Asano, Y. Sugaya, S. Date, N. Kumagai, Y. Ohashi, H. Toyokawa, K. Imai, M. Yosoi,
A. Ichikawa, T. Kishimoto, A. Sakaguchi, M. Sumihama, S. Makino, H. Shimizu
Nuclear Physics A, 670, (2000), 332c-339c[2001]"Photo-Nuclear Reactions at SPring-8"
M. Fujiwara
Nuclear Physics News, 11, (2001), 28-32"Multi-GeV Laser-Electron Photon Project at SPring-8"
T. Nakano, J. Ahn, M. Fujiwara, H. Kohri, N. Matsuoka, T. Mibe, N. Muramatsu, M. Nomachi, H.
Shimizu, K. Yonehara, M. Yosoi, T. Yorita, W. Chang, C. Wang, S. Wang, Y. Asano, T. Hotta, Y.
Sugaya, R. Zegers, S. Date, N. Kumagai, Y. Ohashi, H. Ohkuma, H. Toyokawa, T. Iwata, M. Miyabe,
Y. Miyachi, A. Wakai, K. Imai, T. Ishikawa, M. Miyabe, T. Sasaki, H. Kawai, T. Ooba, Y. Shiino, M.
Wada, Hyong C. Bhang, Z. Y. Kim, A. Sakaguchi, M. Sumihama, K. Hicks, H. Akimune, T.
Matsumura, C. Rangacharyulu, S. Makino
Nuclear Physics A, 684, (2001), 71c-79c"DAQ System for LEPS Experiment"
Y. Sugaya, J. Ahn, H. Akimune, Y. Asano, W. Chang, S. Date, M. Fujiwara, K. Hicks, T. Hotta, K. Imai,
T. Ishikawa, T. Iwata, H. Kawai, Z. Y. Kim, Y. Kishimoto, N. Kumagai, S. Makino, N. Matsukoka, T.
Matsumura, T. Mibe, S. Minami, M. Miyabe, Y. Miyachi, T. Nakano, M. Nomachi, Y. Ohashi, T. Ooba,
C. Rangacharyulu, A. Sakaguchi, T. Sasaki, D. Seki, H. Shimizu, M. Sumihama, H. Toki, T. Toyama,
H. Toyokawa, A. Wakai, C. Wang, C. Wang, T. Yonehara, T. Yorita, M. Yosoi
IEEE Transactions on Nuclear Science, 48, (2001), 1282-1285[2002]"Frontier of Quark-Nuclear Physics at SPring-8 and Nuclear Data"
M. Fujiwara
Journal of Nuclear Science and Technology, Suppl.2, (2002), 580-585"CoherentǾandȁMeson Photoproduction from Deuteron and Nondiffractive Channels"
Alexander I. Titov, M. Fujiwara, T. S. -H. Lee
Physical Review C, 66, (2002), 022202[2003]"Evidence for a Narrow S = +1 Baryon Resonance in Photoproduction from the Neutron"
T. Nakano, D. Ahn, J. Ahn, H. Akimune, Y. Asano, W. Chang, S. Date, H. Ejiri, H. Fujimura, M.
Fujiwara, K. Hicks, T. Hotta, K. Imai, T. Ishikawa, T. Iwata, H. Kawai, Z. Y. Kim, K. Kino, H. Kohri, N.
Kumagai, S. Makino, T. Matsumura, N. Matsuoka, T. Mibe, K. Miwa, M. Miyabe, Y. Miyauchi, M.
Morita, N. Muramatsu, M. Niiyama, M. Nomachi, Y. Ohashi, T. Ooba, H. Ohkuma, Dmitry S. Oshuev,
C. Rangacharyulu, A. Sakaguchi, T. Sasaki, Peter M. Shagin, Y. Shiino, H. Shimizu, Y. Sugaya, M.
Sumihama, H. Toyokawa, A. Wakai
Physical Review Letters, 91, (2003), 012002

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[2]

[3]

[2001]"The Structure of the Archaebacterial Ribosomal Protein S7 and Its Possible Interaction with 16SrRNA"
H. Hosaka, M. Yao, M. Kimura, I. Tanaka
The Journal of Biochemistry, 130, (2001), 695-701[2002]"Structure of the Inositol 1,4,5-Trisphosphate Receptor Binding Core in Complex with Its Ligand"I. Bosanac, J. Alattia, Tapas K. Mal, J. Chan, S. Talarico, Frances K. Tong, Kit I. Tong, F. Yoshikawa,T. Furuichi, M. Iwai, T. Michikawa, K. Mikoshiba, M. Ikura
Nature, 420, (2002), 696-700"Crystal Structure of Archaeosine tRNA-Guanine Transglycosylase"
R. Ishitani, O. Nureki, S. Fukai, T. Kijimoto, N. Nameki, M. Watanabe, H. Kondo, M. Seike, N. Okada,S. Nishimura, S. Yokoyama
Journal of Molecular Biology, 318, (2002), 665-677

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[9]

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[16]

[17]

[18]

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[20]

"X-Ray Snapshots of Quinone Cofactor Biogenesis in Bacterial Copper Amine Oxidase"
M. Kim, T. Okajima, S. Kishishita, M. Yoshimura, A. Kawamori, K. Tanizawa, H. Yamaguchi
Nature Structural Biology, 9, (2002), 591-596"Crystal Structure of C4 Form Maize and Quaternary Complex of E.coli Phosphoenolpyruvate
Carboxylases"
H. Matsumura, Y. Xie, S. Shirakata, T. Inoue, T. Yoshinaga, Y. Ueno, K. Izui, Y. Kai
Structure, 10, (2002), 1721-1730"Crystal Structure of Bacterial Multidrug Efflux Transporter AcrB"
S. Murakami, R. Nakashima, E. Yamashita, A. Yamaguchi
Nature, 419, (2002), 587-593"Structural Basis for the Accessory Protein Recruitment by the ǫ-Adaptin Ear Domain"
T. Nogi, Y. Shiba, M. Kawasaki, T. Shiba, N. Matsugaki, N. Igarashi, M. Suzuki, R. Kato, H. Takatsu,
K. Nakayama, S. Wakatsuki
Nature Structural Biology, 9, (2002), 527-531"Structural Changes in the Calcium Pump Accompanying the Dissociation of Calcium"
C. Toyoshima, H. Nomura
Nature, 418, (2002), 605-611"The Structure of the Mammalian 20S Proteasome at 2.75 Å Resolution"
M. Unno, T. Mizushima, Y. Morimoto, Y. Tomisugi, K. Tanaka, N. Yasuoka, T. Tsukihara
Structure, 10, (2002), 609-618"Crystal Structure of a Bacterial RNA Polymerase Holoenzyme at 2.6 Å Resolution"
Dmitry G. Vassylyev, S. Sekine, O. Laptenko, J. Lee, Marina N. Vassylyeva, S. Borukhov, S.
Yokoyama
Nature, 417, (2002), 712-719[2003]Val"Mechanism of Molecular Interactions for tRNA Recognition by valyl-tRNA Synthetase"
S. Fukai, O. Nureki, S. Sekine, A. Shimada, Dmitry G. Vassylyev, S. Yokoyama
RNA, 9, (2003), 100-111"Mechanism of Metal Activation of Human Hematopoietic Prostaglandin D Synthase"
T. Inoue, D. Irikura, N. Okazaki, S. Kinugasa, H. Matsumura, N. Uodome, M. Yamamoto, T.
Kumasaka, M. Miyano, Y. Kai, Y. Urade
Nature Structural Biology, 10, (2003), 291-296"Structure of the Cytochrome b6f Complex of Oxygenic Photosynthesis: Tuning the Cavity"
G. Kurisu, H. Zhang, Janet L. Smith, William A. Cramer
Science, 302, (2003), 1009-1014"The Structural of Importin-ǪBound to SREBP-2: Nuclear Import of a Transcription Factor"
S. Lee, T. Sekimoto, E. Yamashita, E. Nagoshi, A. Nakagawa, N. Imamoto, M. Yoshimura, H. Sakai,
K. Chong, T. Tsukihara, Y. Yoneda
Science, 302, (2003), 1571-1575"Crystallization and Preliminary X-Ray Crystallographic Analysis of Plant Ferritin from Glycine Max"
T. Masuda, B. Mikami, F. Goto, T. Yoshihara, S. Utsumi
Biochimica et Biophysica Acta - Proteins and Proteomics, 1645, (2003), 113-115"Crystal Structure of AlgQ2, a Macromolecule (Alginate)-binding Protein of Sphingomonas sp. A1,
Complexed with an Alginate Tetrasaccharide at 1.6 Å Resolution"
Y. Mishima, K. Momma, W. Hashimoto, B. Mikami, K. Murata
The Journal of Biological Chemistry, 278, (2003), 6552-6559"X-ray Crystal Structure of IRF-3 and its Functional Implications"
K. Takahasi, N. Noda, M. Horiuchi, W. Suhara, Y. Okabe, Y. Fukuhara, H. Terasawa, S. Akira, T.
Fujita, F. Inagaki
Nature Structural and Molecular Biology, 10, (2003), 922-927"Cloning, Expression, Purification, Crystallization and Initial Crystallographic Analysis of the
Lysinebiosynthesis LysX Protein from Thermus thermophilus HB8"
M. Vassylyeva, H. Sakai, T. Matsuura, S. Sekine, M. Nishiyama, T. Terada, M. Shirouzu, S.
Kuramitsu, D. Vassylyev, S. Yokoyama
Acta Crystallographica Section D, 59, (2003), 1651-1652"Crystallization and Preliminary X-ray Analysis of TBP-Interacting Protein from the Hyperthermophilic
Archaeon Thermococcus kodakaraensis Starain KOD1"
T. Yamamoto, T. Matsuda, N. Sakamoto, H. Matsumura, T. Inoue, M. Morikawa, S. Kanaya, Y. Kai
Acta Crystallographica Section D, 59, (2003), 372-374"Change in the Crystal Packing of SoybeanǪ-amylase Mutants Substituted on a few Surface Amino
Acid Residues"
K. You-Na, M. Adachi, B. Mikami, S. Utsumi
Protein Engineering Design and Selection, 16, (2003), 809-819

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[25]

[26]

Contract Beamlines

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[29]

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[31]

[32]

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[35]

"A Defined Protein-Detergent-Lipid Complex for Crystallization of Integral Membrane Proteins: The
Cytochrome b6f Complex of Oxygenic Photosynthesis"
H. Zhang, G. Kurisu, Janet L. Smith, William A. Cramer
Proceedings of the National Academy of Sciences of the United States of America, 100, (2003),
5160-5163[2004]"Complex Structures of Thermoactinomyces vulgaris R-47 ǩ-Amylase 1 with Malto-Oligosaccharides
Demonstrate the Role of Domain N Acting as a Starch-Binding Domain"
A. Abe, T. Tonozuka, Y. Sakano, S. Kamitori
Journal of Molecular Biology, 335, (2004), 811-822"Crystal Structure of the Membrane Fusion Protein, MexA, of the Multidrug Transporter inPseudomonas aeruginosa"
H. Akama, T. Matsuura, S. Kashiwagi, H. Yoneyama, S. Narita, T. Tsukihara, A. Nakagawa, T. Nakae
The Journal of Biological Chemistry, 279, (2004), 25939-25942"Crystal Structure of the Drug Discharge Outer Membrane Protein, OprM, of Pseudomonas aeruginosa:
Dual Modes of Membrane Anchoring and Occluded Cavity End"H. Akama, M. Kanemaki, M. Yoshimura, T. Tsukihara, T. Kashiwagi, H. Yoneyama, S. Narita, A.
Nakagawa, T. Nakae
The Journal of Biological Chemistry, 279, (2004), 52816-52819"Crystal Structure of the CP1 Domain from Thermus thermophilus Isoleucyl-tRNA Synthetase and its
Complex with L-Valine"
R. Fukunaga, S. Fukai, R. Ishitani, O. Nureki, S. Yokoyama
The Journal of Biological Chemistry, 279, (2004), 8396-8402"The Crystal Structure of the Tryptophan SynthaseǪ2 Subunit from the Hyperthermophile pyrococcus
furiosus Investigation of Stabilization Factors"
Y. Hioki, K. Ogasahara, S. Lee, J. Ma, M. Ishida, Y. Yamagata, Y. Matsuura, M. Ota, M. Ikeguchi, S.
Kuramitsu, K. Yutani
European Journal of Biochemistry, 271, (2004), 2624-2635"Scaling of One-Shot Oscillation Images with a Reference Data Set"
K. Hirata, E. Yamashita, H. Aoyama, K. Muramoto, S. Yoshikawa, T. Tsukihara
Journal of Synchrotron Radiation, 11, (2004), 60-63"A Redox-controlled Molecular Switch Revealed by the Crystal Structure of a Bacterial Heme PAS
Sensor"H. Kurokawa, D. Lee, M. Watanabe, I. Sagami, B. Mikami, C. S. Raman, T. Shimizu
The Journal of Biological Chemistry, 279, (2004), 20186-20193"Crystallization and Preliminary Crystallographic Analysis of Rat Monoamine Oxidase A Complexedwith Clorgyline"
J. Ma, F. Kubota, M. Yoshimura, E. Yamashita, A. Nakagawa, A. Ito, T. Tsukihara
Acta Crystallographica Section D, 60, (2004), 317-319"Structure of Rat Monoamine Oxidase A and Its Specific Recognitions for Substrates and Inhibitors"
J. Ma, M. Yoshimura, E. Yamashita, A. Nakagawa, A. Ito, T. Tsukihara
Journal of Molecular Biology, 338, (2004), 103-114"Strycuture of the Core Region of the SoybeanǪ-Conglycinin ǩ′ Subunit"
Y. Maruyama, N. Maruyama, B. Mikami, S. Utsumi
Acta Crystallographica Section D, 60, (2004), 289-297"Mutational Analysis of the Damage-recognition and Catalytic Mechanism of Human SMUG1 DNA
Glycosylase"
M. Matsubara, T. Tanaka, H. Terato, E. Ohmae, S. Izumi, K. Katayanagi, H. Ide
Nucleic Acids Research, 32, (2004), 5291-5302"Extramembrane Central Pore of Multidrug Exporter AcrB in Escherichia coli Plays an Important Rolein Drug Transport"
S. Murakami, N. Tamura, A. Saito, T. Hirata, A. Yamaguchi
The Journal of Biological Chemistry, 279, (2004), 3743-3748"Crystallization and Preliminary X-ray Analysis of Escherichia coli MutT in Binary and Ternary Complex
Forms"
T. Nakamura, T. Doi, M. Sekiguchi, Y. Yamagata
Acta Crystallographica Section D, 60, (2004), 1641-1643"Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Repeating Sequence at 1.26 Å
Resolution: Implications for Proline Ring Puckering"
K. Okuyama, C. Hongo, R. Fukushima, G. Wu, H. Narita, K. Noguchi, Y. Tanaka, N. Nishino
Biopolymers, 76, (2004), 367-377

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[38]

[39]

[40]

[41]

[42]

[43]

[44]

[45]

[46]

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[48]

[49]

"Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the
Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms"
Y. Shomura, T. Yoshida, R. Iizuka, T. Maruyama, M. Yohda, K. Miki
Journal of Molecular Biology, 335, (2004), 1265-1278"The Low-Spin Heme of Cytochrome c Oxidase as the Driving Element of the Proton-Pumping
Process"
T. Tsukihara, K. Shimokata, Y. Katayama, H. Shimada, K. Muramoto, H. Aoyama, M. Mochizuki, K.
Shinzawa-Itoh, E. Yamashita, M. Yao, Y. Ishimura, S. Yoshikawa
Proceedings of the National Academy of Sciences of the United States of America, 100, (2004),
15304-15309"Structural Basis for Template-Independent RNA Polymerization"
K. Tomita, S. Fukai, R. Ishitani, T. Ueda, N. Takeuchi, Dmitry G. Vassylyev, O. Nureki
Nature, 430, (2004), 700-704"Crystal Structure of the Hemolytic Lectin CEL-III Isolated from the Marine Invertebrate Cucumariaechinata: Implications of Domain Structure for Its Membrane Pore-Formation Mechanism"T. Uchida, T. Yamasaki, S. Eto, H. Sugawara, G. Kurisu, A. Nakagawa, M. Kusunoki, T. Hatakeyama
The Journal of Biological Chemistry, 279, (2004), 37133-37141
phox"A Molecular Mechanism for Autoinhibition of the Tandem SH3 Domains of p47 , the Regulatory
Subunit of the Phagocyte NADPH Oxidase"
S. Yuzawa, N. Suzuki, Y. Fujioka, K. Ogura, H. Sumimoto, F. Inagaki
Genes to Cells, 9, (2004), 443-456[2005]"Complexes of Thermoactinomyces vulgaris R-47 ǩ-amylase 1 and Pullulan Model Oligosaccharides
Provide New Insight into the Mechanism for Recognizing Substrates with ǩ-(1,6) Glycosidic Linkages"
A. Abe, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
The FEBS Journal, 272, (2005), 6145-6153"Preliminary Crystallographic Analysis of the Antibiotic Discharge Outer Membrane Lipoprotein OprM
of Pseudomonas aeruginosa with an Exceptionally Long Unit Cell and Complex Lattice Structure"
H. Akama, m. kanemaki, T. Tsukihara, A. Nakagawa, T. Nakae
Acta Crystallographica Section F, 61, (2005), 131-133"Overproduction and Preliminary Crystallographic Study of a Human Kynurenine Aminotransferase II
Homologue from Pyrococcus horikoshii OT3"
H. Chon, H. Matsumura, S. Shimizu, Y. Koga, K. Takano, N. Maeda, S. Kanaya
Acta Crystallographica Section F, 61, (2005), 319-322"Crystallization and Preliminary X-ray Diffraction Study of Thermostable RNase HIII from Bacillus
stearothermophilus"
H. Chon, H. Matsumura, Y. Koga, K. Takano, S. Kanaya
Acta Crystallographica Section F, 61, (2005), 293-295"Crystal Structure of Lipoate-Protein Ligase A from Escherichia coli: Determination of the Lipoic
Acid-Binding Site"
K. Fujiwara, S. Toma, K. Okamura-Ikeda, Y. Motokawa, A. Nakagawa, H. Taniguchi
The Journal of Biological Chemistry, 280, (2005), 33645-33651"Repetitive Interactions Observed in the Crystal Structure of a Collagen-Model Peptide,[(Pro-Pro-Gly)9]3"
C. Hongo, K. Noguchi, O. Kenji, Y. Tanaka, N. Nishino
The Journal of Biochemistry, 138, (2005), 135-144"Crystal Structure of Human T-Protein of Glycine Cleavage System at 2.0 Å Resolution and its
Implication for Understanding Non-Ketotic Hyperglycinemia"
K. Ikeda-Okumura, H. Hosaka, M. Yoshimura, E. Yamashita, S. Toma, A. Nakagawa, K. Fujiwara, Y.
Motokawa, H. Taniguchi
Journal of Molecular Biology, 351, (2005), 1146-1159"Expression, Purification and Crystallization of Trypanosoma cruzi Dihydroorotate Dehydrogenase
Complexed with Orotate"
D. Inaoka, E. Takashima, A. Osanai, H. Shimizu, T. Nara, T. Aoki, S. Harada, K. Kita
Acta Crystallographica Section F, 61, (2005), 875-878"Crystal Structure of a Human Kynurenine Aminotransferase II Homologue from Pyrococcus horikoshii
OT3 at 2.20 Å Resolution"
S. Kanaya, H. Chon, H. Matsumura, Y. Koga, K. Takano
Proteins: Structure, Function, and Bioinformatics, 61, (2005), 685-688

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[51]

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[54]

[55]

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Contract Beamlines

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[64]

"Structure of the Central Hub of Bacteriophage Mu Baseplate Determined by X-ray Crystallography of
gp44"
Y. Kondou, D. Kitazawa, S. Takeda, Y. Tsuchiya, E. Yamashita, M. Mizuguchi, K. Kawano, T.
Tsukihara
Journal of Molecular Biology, 352, (2005), 976-985"A Structural Basis of Equisetum arvense Ferredoxin Isoform II Producing an Alternative Electron+Transfer with Ferredoxin-NADP Reductase"
G. Kurisu, D. Nishiyama, M. Kusunoki, S. Fujikawa, M. Katoh, G. Hanke, T. Hase, K. Teshima
The Journal of Biological Chemistry, 280, (2005), 2275-2281"Conformational Changes in the Tryptophan Synthase from a Hyperthermophile upon ǩ2Ǫ2 Complex
Formation: Crystal Structure of the Complex"
S. Lee, K. Ogasahara, J. Ma, K. Nishio, M. Ishida, Y. Yamagata, T. Tsukihara, K. Yutani
Biochemistry, 44, (2005), 11417-11427"Crystal Structure of Bacillus sp. GL1 Xanthan Lyase Complexed with a Substrate: Insights into the
Enzyme Reaction Mechanism"
Y. Maruyama, W. Hashimoto, B. Mikami, K. Murata
Journal of Molecular Biology, 350, (2005), 974-986"Direct Evidence for Sphingomonas sp. A1 Periplasmic Proteins as Macromolecule-Binding Proteins
Associated with the ABC Transporter: Molecular Insights into Alginate Transport in the Periplasm"
K. Momma, Y. Mishima, W. Hashimoto, B. Mikami, K. Murata
Biochemistry, 44, (2005), 5053-5064"Conformational Changes in the ǩ-Subunit Coupled to Binding of theǪ2-Subunit of Tryptophan
Synthase from Escherichia coli: Crystal Structure of the Tryptophan Synthase ǩ-Subunit Alone"
K. Nishio, Y. Morimoto, M. Ishizuka, K. Ogasahara, T. Tsukihara, K. Yutani
Biochemistry, 44, (2005), 1184-1192"Crystallization and Preliminary X-ray Crystallographic Analysis of Extracellular Giant Hemoglobinfrom Pogonophoran Oligobrachia mashikoi "N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, K. Miki
Biochimica et Biophysica Acta - Proteins and Proteomics, 1750, (2005), 173-176"Structure of an Extracellular Giant Haemoglobin of the Gutless Beard Worm Oligobrachia mashikoi "N. Numoto, T. Nakagawa, A. Kita, Y. Sasayama, Y. Fukumori, K. Miki
Proceedings of the National Academy of Sciences of the United States of America, 102, (2005),
14521-14526"Reinvestigation of Metal Ion Specificity for Quinone Cofactor Biogenesis in Bacterial Copper Amine
Oxidase"T. Okajima, S. Kishishita, G. Kyu, T. Murakawa, M. Kim, H. Yamaguchi, S. Hirota, S. Kuroda, K.
Tanizawa
Biochemistry, 44, (2005), 12041-12048"Observation of the Transient Rotator Phase of n-Hexadecane in Emulsified Droplets with
Time-Resolved Two-Dimensional Small- and Wide-Angle X-Ray Scattering"
Y. Shinohara, N. Kawasaki, S. Ueno, I. Kobayashi, M. Nakajima, Y. Amemiya
Physical Review Letters, 94, (2005), 097801"Structure of the Blue Cornflower Pigment"
M. Shiono, N. Matsugaki, K. Takeda
Nature, 436, (2005), 791"Crystallization and Preliminary X-ray Analysis of Methylthioribose-1-phosphate Isomerase from
Bacillus subtils"
H. Tamura, T. Inoue, H. Matsumura, H. Ashida, Y. Saito, A. Yokota, Y. Kai
Acta Crystallographica Section F, 61, (2005), 595-598"The Crystal Structures of Semi-Synthetic Aequorins"
S. Toma, K. Teranishi, K. Chong, A. Nakagawa, S. Inoue, O. Shimomura
Protein Science, 14, (2005), 409-416
2+"Identification of Single Mn Binding Sites in the Mutant Proteins of E. coli RNase HI at Glu48 and/or
Asp134 by X-ray Crystallography"
Y. Tsunaka, K. Takano, H. Matsumura, Y. Yamagata, S. Kanaya
Journal of Molecular Biology, 345, (2005), 1171-1183"Crystal Structure of Escherichia coli SufA Involved in Biosynthesis of Iron-Sulfur Clusters: Implication
for a Functional Dimer"
K. Wada, Y. Hasegawa, Z. Gong, Y. Minami, K. Fukuyama, Y. Takahashi
FEBS Letters, 579, (2005), 6543-6548

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"Absolute Configuration of the Hydroxyfarnesylethyl Group of Haem A, Determined by X-ray
Structural Analysis of Bovine Heart Cytochrome c Oxidase using Methods Applicable at 2.8 Å
Resolution"
E. Yamashita, H. Aoyama, M. Yao, K. Muramoto, K. Itoh-Shinzawa, S. Yoshikawa, T. Tsukihara
Acta Crystallographica Section D, 61, (2005), 1373-1377[2006]"Kinetic and Structural Studies on the Catalytic Role of the Aspartic Acid Residue Conserved in
Copper Amine Oxidase"
Y. Chiu, T. Okajima, T. Murakawa, M. Uchida, M. Taki, S. Hirota, M. Kim, H. Yamaguchi, Y. Kawano,N. Kamiya, S. Kuroda, H. Hayashi, Y. Yamamoto, K. Tanizawa
Biochemistry, 45, (2006), 4105-4120"Crystal Structure and Structure-based Mutational Analyses of RNase HIII from Bacillus
stearothermophilus: A New Type 2 RNase H with TBP-like Substrate-binding Domain at the N
Terminus"
H. Chon, H. Matsumura, Y. Koga, K. Takano, S. Kanaya
Journal of Molecular Biology, 356, (2006), 165-178"Structure of Dimerized Radixin FERM Domain Suggests a Novel Masking Motif in C-terminal
Residues 295-304"
T. Hakoshima, F. Yusa, K. Kitano
Acta Crystallographica Section F, 62, (2006), 340-345"Targeting AMAP1 and Cortactin Binding Bearing an Atypical src Homology 3/proline Interface forPrevention of Breast Cancer Invasion and Metastasis"
S. Hashimoto, M. Hirose, A. Hashimoto, M. Morishige, A. Yamada, H. Hosaka, K. Akagi, E. Ogawa, C.
Oneyama, T. Agatsuma, M. Okada, H. Kobayashi, H. Wada, H. Nakano, T. Ikegami, A. Nakagawa, H.
Sabe
Proceedings of the National Academy of Sciences of the United States of America, 103, (2006),
7036-7041"Crystal Structure of 3-Hydroxybenzoate Hydroxylase from Comamonas testosteroni Has a Large
Tunnel for Substrate and Oxygen Access to the Active Site"
T. Hiromoto, S. Fujiwara, K. Hosokawa, H. Yamaguchi
Journal of Molecular Biology, 364, (2006), 878-896"Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Diuslfide Bond Generation"
K. Inaba, S. Murakami, M. Suzuki, A. Nakagawa, E. Yamashita, K. Okada, K. Ito
Cell, 127, (2006), 789-801"Completely Buried, Non-Ion-Paired Glutamic Acid Contributes Favorably to the Conformational
Stability of Pyrrolidone Carboxyl Peptidases from Hyperthermophiles"
J. Kaushik, S. Iimura, K. Ogasahara, Y. Yamagata, S. Segawa, K. Yutani
Biochemistry, 45, (2006), 7100-7112"Conformation of Amyloid Fibrils ofǪ2-Microglobulin Probed by Tryptophan Mutagenesis"
M. Kihara, E. Chitani, K. Iwata, K. Yamamoto, T. Matsuura, A. Nakagawa, H. Naiki, Y. Goto
The Journal of Biological Chemistry, 281, (2006), 31061-31069"The Crystal Structure of Human Atg4b, a Processing and De-conjugating Enzyme for
Autophagosomeforming Modifiers"
T. Kumanomidou, T. Mizushima, M. Komatsu, A. Suzuki, I. Tanida, Y. Sou, T. Ueno, E. Kominami, K.
Tanaka, T. Yamane
Journal of Molecular Biology, 355, (2006), 612-618"Crystal Structure of Intein Homing Endonuclease II Encoded in DNA Polymerase Gene from
Hyperthermophilic Archaeon Thermococcus kodakaraensis Strain KOD1"
H. Matsumura, H. Takahashi, T. Inoue, T. Yamamoto, H. Hashimoto, M. Nishioka, S. Fujiwara, M.
Takagi, T. Imanaka, Y. Kai
Proteins: Structure, Function, and Bioinformatics, 63, (2006), 711-715"A Novel Mechanism of Allosteric Regulation of Archaeal Phosphoenolpyruvate Carboxylase: aCombined Approach to Structure-based Alignment and Model Assessment"
H. Matsumura, K. Izui, K. Mizuguchi
Protein Engineering Design and Selection, 19, (2006), 409-419"Crystallization and X-ray Diffraction Analysis of a Catalytic Domain of Hyperthermophilic Chitinasefrom Pyrococcus furiosus"
S. Mine, T. Nakamura, K. Hirata, K. Ishikawa, Y. Hagihara, K. Uegaki
Acta Crystallographica Section F, 62, (2006), 791-793"Crystallization and Preliminary Crystallographic Studies on the Pasteurella multocida Toxin Catalytic
Domain"M. Miyazawa, K. Kitadokoro, S. Kamitani, H. Shime, Y. Horiguchi
Acta Crystallographica Section F, 62, (2006), 906-908

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"The Asymmetric IscA Homodimer with an Exposed [2Fe-2S] Cluster Suggests the Structural Basis of
the Fe-S Cluster Biosynthetic Scaffold"
K. Morimoto, E. Yamashita, Y. Kondou, T. Tsukihara, S. Lee, F. Arisaka, M. Nakai
Journal of Molecular Biology, 360, (2006), 117-132"Crystal Structures of a Multidrug Transporter Reveal a Functionally Rotating Mechanism"
S. Murakami, R. Nakashima, E. Yamashita, T. Matsumoto, A. Yamaguchi
Nature, 443, (2006), 173-179"Quantum Mechanical Hydrogen Tunneling in Bacterial Copper Amine Oxidase Reaction"
T. Murakawa, T. Okajima, S. Kuroda, T. Nakamoto, M. Taki, Y. Yamamoto, H. Hayashi, K. Tanizawa
Biochemical and Biophysical Research Communications, 342, (2006), 414-423"Crystallization and Preliminary X-ray Analysis of Rat SHPS-1"
A. Nagata, H. Ohnishi, M. Yoshimura, A. Ogawa, S. Ujita, H. Adachi, M. Okada, T. Matozaki, A.
Nakagawa
Acta Crystallographica Section F, 62, (2006), 189-191"Crystallization and Preliminary X-ray Analysis of Human MTH1 Complexed with Two Oxidized
Nucleotides, 8-oxo-dGMP and 2-oxo-dATP"
T. Nakamura, Y. Kitaguchi, M. Miyazawa, H. Kamiya, S. Toma, S. Ikemizu, M. Shirakawa, Y.
Nakabeppu, Y. Yamagata
Acta Crystallographica Section F, 62, (2006), 1283-1285"Single Nucleotide Polymorphism in the Cytolethal Distending Toxin B Gene Confers Heterogeneity in
the Cytotoxicity of Actinobacillus actinomycetemcomitans"
S. Nishikubo, M. Ohara, M. Ikura, K. Katayanagi, T. Fujiwara, H. Komatsuzawa, H. Kurihara, M. Sugai
Infection and Immunity, 74, (2006), 7014-7020"Structure of a Signaling-Competent Reelin Fragment Revealed by X-ray Crystallography andElectron Tomography"
T. Nogi, N. Yasui, K. Iwasaki, M. Hattori, J. Takagi
The EMBO Journal, 25, (2006), 3675-3683"Crystal Structures of Cytochrome cL and Methanol Dehydrogenase from Hyphomicrobium
denitrificans: Structural and Mechanistic Insights into Interactions between the Two Proteins"
M. Nojiri, D. Hira, K. Yamaguchi, T. Okajima, K. Tanizawa, S. Suzuki
Biochemistry, 45, (2006), 3481-3492"Structure of a Complex of Thermoactinomyces vulgaris R-47 ǩ-Amylase 2 with Maltohexaose
Demonstrates the Important Role of Aromatic Residues at the Reducing End of the Substrate Binding
Cleft"
A. Ohtaki, M. Mizuno, H. Yoshida, T. Tonozuka, Y. Sakano, S. Kamitori
Carbohydrate Research, 341, (2006), 1041-1046"Conformation of alloHyp in the Y Position in the Host-guest Peptide with the Pro-Pro-Gly Sequence:
Implication of the Destabilization of (Pro-alloHyp-Gly)10"
K. Okuyama, N. Jiravanichanun, N. Nishino
Biopolymers, 81, (2006), 225-233"Expression, Purification and Crystallization of L-methionine ǫ-lyase 2 from Entamoeba histolytica"
D. Sato, W. Yamagata, K. Kamei, T. Nozaki, S. Harada
Acta Crystallographica Section F, 62, (2006), 1034-1036"Structural Bases of Transfer RNA-dependent Amino Acid Recognition and Activation by
Glutamyl-tRNA Synthetase"
S. Sekine, M. Shichiri, S. Bernier, R. Chênevert, J. Lapointe, S. Yokoyama
Structure, 14, (2006), 1791-1799"Purification, Crystallization and Preliminary X-ray Diffraction of SecDF, a Translocon-AssociatedMembrane Protein, from Thermus thermophilus"
T. Tsukazaki, H. Mori, S. Fukai, T. Numata, A. Perederina, H. Adachi, H. Matsumura, K. Takano, S.
Murakami, T. Inoue, Y. Mori, T. Sasaki, Dmitry G. Vassylyev, O. Nureki, K. Ito
Acta Crystallographica Section F, 62, (2006), 376-380"The Crystal Structure of L-lactate Oxidase from Aerococcus viridans at 2.1 Å Resolution Reveals the
Mechanism of Strict Substrate Recognition"
Y. Umena, K. Yorita, T. Matsuoka, A. Kita, K. Fukui, Y. Morimoto
Biochemical and Biophysical Research Communications, 350, (2006), 249-256"The Crystal Structure of L-lactate Oxidase from Aerococcus viridans at 2.1 Å Resolution Reveals the
Mechanism of Strict Substrate Recognition"
Y. Umena, K. Fukui, A. Kita, K. Yorita, T. Matsuoka, Y. Morimoto
Biochemical and Biophysical Research Communications, 350, (2006), 249-256"Molecular Mechanism for the Regulation of Rho-Kinase by Dimerization and Its Inhibition by Fasudil"
H. Yamaguchi, M. Kasa, M. Amano, K. Kaibuchi, T. Hakoshima
Structure, 14, (2006), 589-600

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"Structural Basis for Induced-fit Binding of Rho-Kinase to the Inhibitor Y-27632"
H. Yamaguchi, Y. Miwa, M. Kasa, K. Kitano, M. Amano, K. Kaibuchi, T. Hakoshima
The Journal of Biochemistry, 140, (2006), 305-311"Crystal Structure of TBP-interacting Protein(Tk-TIP26) and Implications for Its Inhibition Mechanismof the Interaction between TBP and TATA-DNA"
T. Yamamoto, T. Inoue, H. Matsumura, T. Matsuda, S. Kanaya, M. Morikawa, Y. Kai
Protein Science, 15, (2006), 152-161"Reaction Mechanism of Bovine Heart Cytochrome c Oxidase"
S. Yoshikawa, K. Muramoto, K. Shinzawa-Itoh, H. Aoyama, T. Tsukihara, T. Ogura, K. Shimokata, Y.
Katayama, H. Shimada
Biochimica et Biophysica Acta - Bioenergetics, 1757, (2006), 395-400"Proton Pumping Mechanism of Bovine Heart Cytochrome c Oxidase"
S. Yoshikawa, K. Muramoto, K. Shinzawa-Itoh, H. Aoyama, T. Tsukihara, K. Shimokata, Y.
Katayama, H. Shimada
Biochimica et Biophysica Acta - Bioenergetics, 1757, (2006), 1110-1116[2007]"The Crystal Structure of a Virus-like Particle from the Hyperthermophilic Archaeon Pyrococcus furiosus
Provides Insight into the Evolution of Viruses"
F. Akita, K. Chong, H. Tanaka, E. Yamashita, N. Miyazaki, Y. Nakaishi, M. Suzuki, K. Namba, T.
Tsukihara, A. Nakagawa
Journal of Molecular Biology, 368, (2007), 1469-1483"Crystal Structure of Bovine Lipoyltransferase in Complex with Lipoyl-AMP"
K. Fujiwara, H. Hosaka, M. Matsuda, K. Ikeda, Y. Motokawa, M. Suzuki, A. Nakagawa, H. Taniguchi
Journal of Molecular Biology, 371, (2007), 222-234"Crystallographic Characterization of the Radixin FERM Domain Bound to the Cytoplasmic Tails of
Adhesion Molecules CD43 and PSGL-1"
T. Hakoshima, Y. Takai, K. Kitano, S. Terawaki, R. Maesaki
Acta Crystallographica Section F, 63, (2007), 49-51"Crystallographic Evidence for Water-assisted Photo-induced Peptide Cleavage in the Stony Coral
Fluorescent Protein Kaede"
I. Hayashi, H. Mizuno, Kit I. Tong, T. Furuta, F. Tanaka, M. Yoshimura, A. Miyawaki, M. Ikura
Journal of Molecular Biology, 372, (2007), 918-926"Structures and Physiological Roles of All the Integral Lipids of Bovine Heart Cytochrome c Oxidase"
K. Itoh, H. Aoyama, K. Muramoto, H. Terada, T. Kurauchi, Y. Tadehara, A. Yamasaki, T. Sugimura, S.
Kurono, K. Tsujimoto, T. Mizushima, E. Yamashita, T. Tsukihara, S. Yoshikawa
The EMBO Journal, 26, (2007), 1713-1725"High-resolution Crystal Structure ofǪ2-Microglobulin Formed at pH 7.0"
K. Iwata, T. Matsuura, K. Sakurai, A. Nakagawa, Y. Goto
The Journal of Biochemistry, 142, (2007), 413-419"A Snapshot of the 30S Ribosomal Subunit Capturing mRNA via the Shine-Dalgarno Interaction"
T. Kaminishi, D. Wilson, C. Takemoto, J. Harms, M. Kawazoe, F. Schluenzen, K. Hanawa-Suetsugu,
M. Shirouzu, P. Fucini, S. Yokoyama
Structure, 15, (2007), 289-297"Structural, Thermodynamic, and Mutational Analyses of a Psychrotrophic RNase HI"
S. Kanaya, K. Takano, T. Tadokoro, D. You, H. Chon, H. Matsumura, Y. Koga, Y. Abe
Biochemistry, 46, (2007), 7460-7468"Crystallization and Preliminary X-ray Diffraction Study of Glycerol Kinase from the Hyperthermophilic
Archaeon Thermococcus kodakaraensis"
R. Katsumi, Y. Koga, D. You, K. Takano, H. Matsumura, S. Kanaya
Acta Crystallographica Section F, 63, (2007), 126-129"Location of PsbY in Oxygen-evolving Photosystem II Revealed by Mutagenesis and X-ray
Crystallography"
K. Kawakami, M. Iwai, M. Ikeuchi, N. Kamiya, J. Shen
FEBS Letters, 581, (2007), 4983-4987"Crystal Structures Reveal a Thiol Protease-like Catalytic Triad in the C-Terminal Region of
Pasteurella multocida Toxin"
K. Kitadokoro, M. Miyazawa, S. Kamitani, M. Hanajima-Ozawa, A. Fukui, M. Miyake, Y. Horiguchi
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),
5139-5144"Crystallographic Study on the Interaction of L-lactate Oxidase with Pyruvate at 1.9 Å Resolution"
S. Li, Y. Umena, K. Yorita, T. Matsuoka, A. Kita, K. Fukui, Y. Morimoto
Biochemical and Biophysical Research Communications, 358, (2007), 1002-1007

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"Structural Basis for Tubulin Recognition by Cytoplasmic Linker Protein 170 and Its Autoinhibition"
M. Mishima, R. Maesaki, M. Kasa, T. Watanabe, M. Fukata, K. Kaibuchi, T. Hakoshima
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),
10346-10351
Fbs1
Ubiquitin Ligase""Structural Basis for the Selection of Glycosylated Substrates by SCF
T. Mizushima, Y. Yoshida, T. Kumanomidou, Y. Hasegawa, A. Suzuki, T. Yamane, K. Tanaka
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),
5777-5781"Crystal Structure of Ufc1, the Ufm1-conjugating Enzyme"
T. Mizushima, K. Tatsumi, Y. Ozaki, T. Kawakami, A. Suzuki, K. Ogasahara, M. Komatsu, E.
Kominami, K. Tanaka, T. Yamane
Biochemical and Biophysical Research Communications, 362, (2007), 1079-1084"Trapping of a Dopaquinone Intermediate in the TPQ Cofactor Biogenesis in a Copper-containing
Amine Oxidase from Arthrobacter globiformis"
Robyn H. Moore, M. Ashley Spies, Matthew B. Culpepper, T. Murakawa, S. Hirota, T. Okajima, K.
Tanizawa, M. Mure
Journal of the American Chemical Society, 129, (2007), 11524-11534"A Histidine Residue Acting as a Controlling Site for Dioxygen Reduction and Proton Pumping by
Cytochrome c Oxidase"
K. Muramoto, K. Hirata, K. Itoh, S. Yokoo, E. Yamashita, H. Aoyama, T. Tsukihara, S. Yoshikawa
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),7881-7886+"Structural Diversity in the Cytoplasmic Region of G Protein-gated inward Rectifier K Channel"
A. Nakagawa, A. Inanobe, T. Matsuura, Y. Kurachi
Channels, 1, (2007), 39-45"Structure and Function of a Hexameric Copper-Containing Nitrite Reductase"
M. Nojiri, Y. Xie, T. Inoue, T. Yamamoto, H. Matsumura, K. Kataoka, . Deligeer, K. Yamaguchi, Y. Kai,
S. Suzuki
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),
4315-4320"The Proton-pumping Pathway of Bovine Heart Cytochrome c Oxidase"
K. Shimokata, Y. Katayama, H. Murayama, M. Suematsu, T. Tsukihara, K. Muramoto, H. Aoyama, S.
Yoshikawa, H. Shimada
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),
4200-4205"Preparation, Crystallization and Preliminary Crystallographic Analysis of Old Yellow Enzyme from
Trypanosoma cruzi "S. Sugiyama, K. Tokuoka, N. Okamoto, H. Matsumura, N. Uchiyama, Y. Okano, Y. Urade, K. Inaka, T.
Inoue
Acta Crystallographica Section F, 63, (2007), 896-898"Structure of a Receptor-binding Reelin Fragment and Mutational Analysis Reveal a Recognition
Mechanism Similar to Endocytic Receptors"
N. Yasui, T. Nogi, T. Kitao, Y. Nakano, M. Hattori, J. Takagi
Proceedings of the National Academy of Sciences of the United States of America, 104, (2007),9988-9993"Crystal Structure of Type 1 Ribonuclease H from Hyperthermophilic Archaeon Sulfolobus tokodaii:
Role of Arginine 118 and C-terminal Anchoring"
D. You, H. Chon, Y. Koga, K. Takano, S. Kanaya
Biochemistry, 46, (2007), 11494-11503[2008]"Evaluation of the Functional Role of the Heme-6-propionate Side Chain in Cytochrome P450cam"
K. Harada, K. Sakurai, K. Ikemura, T. Ogura, S. Hirota, H. Shimada, T. Hayashi
Journal of the American Chemical Society, 130, (2008), 432-433"Crystal Structures of Lymnaea stagnalis AChBP in Complex with Neonicotinoid Insecticides
Imidacloprid and Clothianidin"
M. Ihara, T. Okajima, A. Yamashita, T. Oda, K. Hirata, H. Nishiwaki, T. Morimoto, M. Akamatsu, Y.
Ashikawa, S. Kuroda, R. Mega, S. Kuramitsu, David B. Sattelle, K. Matsuda
Invertebrate Neuroscience, 8, (2008), 71-81"Novel Cation-ǸInteraction Revealed by Crystal Structure of Thermoalkalophilic Lipase"
H. Matsumura, T. Inoue, T. Yamamoto, T. Leow, T. Mori, A. Salleh, Y. Kai, R. Rahman
Proteins: Structure, Function, and Bioinformatics, 70, (2008), 592-598

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Subtilis: Implications for Catalytic Mechanism"
H. Tamura, T. Inoue, Y. Saito, Y. Kai, H. Ashida, A. Yokota, H. Matsumura
Protein Science, 17, (2008), 126-135"Structural Basis for the Decarboxylation of Orotidine 5’-monophosphate (OMP) by Plasmodium
falciparum OMP Decarboxylase"
K. Tokuoka, Y. Kusakari, Sudaratana R. Krungkrai, H. Matsumura, Y. Kai, J. Krungkrai, T. Horii, T.
Inoue
The Journal of Biochemistry, 143, (2008), 69-78"Crystal Structure of a Chaperone Complex that Contributes to the Assembly of Yeast 20S
Proteasomes"
H. Yashiroda, T. Mizushima, K. Okamoto, T. Kameyama, H. Hayashi, T. Kihsimoto, S. Niwa, M.
Kasahara, E. Kurimoto, E. Sakata, K. Takagi, A. Suzuki, Y. Hirano, S. Murata, K. Kato, T. Yamane, K.
TanakaNature Structural and Molecular Biology, 15, (2008), 228-236

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