Antitubercular Ilamycins from Marine-Derived Streptomyces atratus SCSIO ZH16 ΔilaR
Sun, Changli; Liu, Zhiyong; Zhu, Xiangcheng; Fan, Zhiying; Huang, Xuanmei; Wu, Qiaoling; Zheng, Xiaohong; Qin, Xiangjing; Zhang, Tianyu; Zhang, Hua; Ju, Jianhua; Ma, Junying; Journal of Natural Products  (2020) –; doi:10.1021/acs.jnatprod.0c00151

data_1557883
_publ_section_title
;
 Antitubercular Ilamycins from Marine-Derived Streptomyces atratus SCSIO
 ZH16 \DilaR
;
_journal_name_full               'Journal of Natural Products'
_journal_paper_doi               10.1021/acs.jnatprod.0c00151
_journal_year                    2020
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C54 H75 N9 O13'
_chemical_formula_sum            'C54 H75 N9 O13'
_chemical_formula_weight         1058.23
_space_group_crystal_system      orthorhombic
_space_group_IT_number           18
_space_group_name_Hall           'P 2 2ab'
_space_group_name_H-M_alt        'P 21 21 2'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2020-02-08
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   26.0693(2)
_cell_length_b                   25.2634(2)
_cell_length_c                   19.77155(18)
_cell_measurement_reflns_used    21567
_cell_measurement_temperature    100(8)
_cell_measurement_theta_max      70.9090
_cell_measurement_theta_min      3.8170
_cell_volume                     13021.53(19)
_computing_cell_refinement       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve (Bourhis et al., 2015)'
_diffrn_ambient_temperature      100(8)
_diffrn_measured_fraction_theta_full 0.981
_diffrn_measured_fraction_theta_max 0.981
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
--------------------------------------------------------------------------
  1  \w     81.00 121.00   0.40    5.00    --   42.30  77.00-180.00  100
  2  \w     80.00 132.00   0.40    5.00    --   42.30  77.00 120.00  130
  3  \w     10.00  85.20   0.40    5.00    --   42.30 -82.00 -90.00  188
  4  \w    -33.00  -7.00   0.40    5.00    --   42.30 -82.00 -90.00   65
  5  \w    103.00 131.00   0.40    5.00    --   42.30  77.00-150.00   70
  6  \w     80.00 127.20   0.40    5.00    --   42.30  77.00-120.00  118
  7  \w     86.80 132.00   0.40    5.00    --   42.30  77.00 -60.00  113
  8  \w     80.00 106.00   0.40    5.00    --   42.30  77.00  90.00   65
  9  \w     54.00 190.00   0.40   30.00    --  101.00  38.00-120.00  340
 10  \w     53.00 123.00   0.40   30.00    --  101.00 -63.00  60.00  175
 11  \w    100.00 126.00   0.40   30.00    --  101.00  82.00-180.00   65
 12  \w     25.00 144.20   0.40   30.00    --  101.00 -38.00-150.00  298
 13  \w    111.00 152.20   0.40   30.00    --  101.00  82.00 -60.00  103
 14  \w     81.00 165.00   0.40   30.00    --  101.00  38.00 -90.00  210
 15  \w    133.00 189.00   0.40   30.00    --  101.00  82.00-180.00  140
 16  \w     56.00 127.20   0.40   30.00    --  101.00 -50.00-150.00  178
 17  \w     15.00  41.00   0.40   30.00    --  101.00 -50.00-150.00   65
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0559
_diffrn_reflns_av_unetI/netI     0.0626
_diffrn_reflns_Laue_measured_fraction_full 0.981
_diffrn_reflns_Laue_measured_fraction_max 0.981
_diffrn_reflns_limit_h_max       31
_diffrn_reflns_limit_h_min       -30
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -25
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            63922
_diffrn_reflns_point_group_measured_fraction_full 0.978
_diffrn_reflns_point_group_measured_fraction_max 0.978
_diffrn_reflns_theta_full        67.078
_diffrn_reflns_theta_max         67.078
_diffrn_reflns_theta_min         3.816
_exptl_absorpt_coefficient_mu    0.640
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.46003
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.33c (Rigaku Oxford Diffraction, 2017)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.080
_exptl_crystal_description       plate
_exptl_crystal_F_000             4528
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_platon_squeeze_details
;
TITL sunchangliP 21 21 2llecR = 0.05
CELL   26.0693   25.2634   19.7715     90.00     90.00     90.00
SPGR P21212
C101 0.553 0.913 0.626 !      11.20 eA-3
Q102 0.232 0.314 0.565 !       9.74 eA-3
C103 0.031 0.893 0.872 !       8.80 eA-3
C104 0.290 0.617 0.687 !       7.31 eA-3
C105 0.579 0.961 0.640 !       7.14 eA-3
C106 0.181 0.299 0.902 !       6.53 eA-3
C107 0.077 0.501 0.402 !       5.91 eA-3
C108 0.046 0.438 0.030 !       5.71 eA-3
C109 0.805 0.925 0.300 !       5.12 eA-3
C110 0.302 0.566 0.782 !       4.59 eA-3
C111 1.000 0.501 0.172 !       4.52 eA-3
Q112 0.094 0.889 0.641 !       3.99 eA-3
C113 0.736 0.161 0.376 !       3.78 eA-3
C114 0.432 0.940 0.091 !       3.62 eA-3
C115 0.931 0.529 0.990 !       3.58 eA-3
C116 0.962 0.064 0.873 !       3.56 eA-3
C117 0.265 0.378 0.638 !       3.51 eA-3
C118 0.975 0.473 0.122 !       2.93 eA-3
C119 0.287 0.860 0.388 !       2.55 eA-3
C120 0.164 0.354 0.829 !       2.43 eA-3
Q121 0.016 0.945 0.799 !       2.41 eA-3
C122 0.813 0.883 0.187 !       2.27 eA-3
C123 0.990 0.444 0.160 !       2.21 eA-3
C124 0.319 0.792 0.156 !       2.20 eA-3
Q125 0.585 0.034 0.973 !       2.08 eA-3
C126 0.701 0.169 0.137 !       1.97 eA-3
C127 0.265 0.333 0.676 !       1.81 eA-3
C128 0.687 0.149 0.223 !       1.71 eA-3
C129 0.302 0.365 0.672 !       1.28 eA-3
C130 0.225 0.927 0.328 !       1.25 eA-3
C131 0.322 0.898 0.198 !       1.16 eA-3
C132 0.619 0.106 0.170 !       1.09 eA-3
C133 0.928 0.479 0.310 !       1.01 eA-3
C134 0.094 0.463 0.397 !       0.91 eA-3
C135 0.990 0.506 0.947 !       0.82 eA-3
C136 0.034 0.501 0.404 !       0.74 eA-3
C137 0.956 0.522 0.401 !       0.70 eA-3
Q138 0.650 0.992 0.797 !       0.69 eA-3
C139 0.025 0.466 0.981 !       0.68 eA-3
Q140 0.844 0.920 0.843 !       0.68 eA-3
Q141 0.094 0.996 0.873 !       0.63 eA-3
C142 0.756 0.206 0.337 !       0.63 eA-3
C143 0.598 0.065 0.127 !       0.62 eA-3
C144 0.515 0.030 0.950 !       0.55 eA-3
C145 0.781 0.592 0.581 !       0.54 eA-3
Q146 0.071 0.963 0.870 !       0.52 eA-3
C147 0.232 0.349 0.893 !       0.51 eA-3
;
_refine_diff_density_max         0.590
_refine_diff_density_min         -0.279
_refine_diff_density_rms         0.042
_refine_ls_abs_structure_details
;
 Flack x determined using 7417 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.17(6)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.008
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1430
_refine_ls_number_reflns         22740
_refine_ls_number_restraints     5
_refine_ls_restrained_S_all      1.008
_refine_ls_R_factor_all          0.0596
_refine_ls_R_factor_gt           0.0494
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0851P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1273
_refine_ls_wR_factor_ref         0.1335
_reflns_Friedel_coverage         0.848
_reflns_Friedel_fraction_full    0.975
_reflns_Friedel_fraction_max     0.975
_reflns_number_gt                19238
_reflns_number_total             22740
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np0c00151_si_002.cif
_cod_data_source_block           sunchangli_2l-2c_collect_sq
_cod_original_cell_volume        13021.5(2)
_cod_database_code               1557883
_shelx_shelxl_version_number     2016/6
_shelx_estimated_absorpt_t_max   0.969
_shelx_estimated_absorpt_t_min   0.939
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, {H13A,H13B,H13C} of C13A, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All O(H) groups, {H53D,H53E,H53F} of C53, {H16E,H16F,H16G} of C16, {H53A,
  H53B,H53C} of C53A, {H37A,H37B,H37C} of C37A, {H34D,H34E,H34F} of C34, {H15C,
  H15D,H15E} of C15A, {H51D,H51E,H51F} of C51, {H28D,H28E,H28F} of C28, {H16A,
  H16B,H16C} of C16A, {H52A,H52B,H52C} of C52A, {H52D,H52E,H52F} of C52, {H27D,
  H27E,H27F} of C27, {H27A,H27B,H27C} of C27A, {H28A,H28B,H28C} of C28A, {H37D,
  H37E,H37F} of C37, {H34A,H34B,H34C} of C34A, {H54D,H54E,H54F} of C54, {H54A,
  H54B,H54C} of C54A, {H51A,H51B,H51C} of C51A, {H22D,H22E,H22F} of C22, {H0AB,
  H0AC,H0AD} of C0AA, {H22A,H22B,H22C} of C22A
2. Restrained distances
 C13A-O0AA
 1.45 with sigma of 0.01
 C15A-O2A
 1.45 with sigma of 0.02
 C20-C73
 1.3 with sigma of 0.02
 C73-C0AA
 1.5 with sigma of 0.02
 O2A-C15A
 1.45 with sigma of 0.01
3. Uiso/Uaniso restraints and constraints
Uanis(C14A) = Uanis(C3AA)
Uanis(O2A) = Uanis(O0AA)
4. Others
 Sof(H16D)=Sof(H13B)=Sof(H13C)=Sof(H15C)=Sof(H15D)=Sof(H15E)=Sof(C3AA)=
 Sof(H3AC)=Sof(H3AD)=Sof(O0AA)=Sof(H0AA)=1-FVAR(1)
 Sof(H16A)=Sof(H16B)=Sof(H16C)=Sof(H13A)=Sof(H15A)=Sof(H15B)=Sof(O2A)=
 Sof(H2AB)=Sof(C14A)=Sof(H14A)=Sof(H14B)=FVAR(1)
 Sof(H20B)=Sof(C21)=Sof(H21)=Sof(C22)=Sof(H22D)=Sof(H22E)=Sof(H22F)=1-FVAR(2)
 Sof(H20)=Sof(C73)=Sof(H73)=Sof(C0AA)=Sof(H0AB)=Sof(H0AC)=Sof(H0AD)=FVAR(2)
5.a Ternary CH refined with riding coordinates:
 C39A(H39A), C30(H30), C2(H2C), C24(H24), C30A(H30A), C32(H32), C24A(H24A),
 C18A(H18A), C48(H48), C18(H18), C36A(H36A), C48A(H48A), C36(H36), C2A(H2AA),
 C32A(H32A), C39(H39), C26A(H26A), C26(H26), C50(H50), C50A(H50A)
5.b Secondary CH2 refined with riding coordinates:
 C31(H31C,H31D), C15(H15F,H15G), C3(H3B,H3C), C31A(H31A,H31B), C49A(H49A,H49B),
  C25A(H25A,H25B), C40A(H40A,H40B), C25(H25C,H25D), C3A(H3AA,H3AB), C19(H19C,
 H19D), C49(H49C,H49D), C19A(H19A,H19B), C40(H40C,H40D), C13A(H13B,H13C),
 C15A(H15A,H15B)
5.c Aromatic/amide H refined with riding coordinates:
 N2(H2B), N6A(H6A), N4A(H4A), N3(H3), N2A(H2A), N6(H6), N3A(H3A), N4(H4),
 N8A(H8A), N8(H8), C13(H13), C4(H4B), C4A(H4AA), C45A(H45A), C42A(H42A),
 C46A(H46A), C10(H10), C7(H7B), C42(H42), C45(H45), C7A(H7A), C8(H8B),
 C20A(H20A), C46(H46), C10A(H10A), C9(H9), C21A(H21A), C20(H20), C20(H20B),
 C16A(H16D), C8A(H8AA), C9A(H9A), C13A(H13A), C73(H73), C21(H21)
5.d Tetrahedral OH refined with riding coordinates:
 O2A(H2AB), O0AA(H0AA)
5.e X=CH2 refined with riding coordinates:
 C14A(H14A,H14B), C3AA(H3AC,H3AD)
5.f Idealised Me refined as rotating group:
 C53A(H53A,H53B,H53C), C16(H16E,H16F,H16G), C53(H53D,H53E,H53F), C37A(H37A,
 H37B,H37C), C34(H34D,H34E,H34F), C54A(H54A,H54B,H54C), C54(H54D,H54E,H54F),
 C34A(H34A,H34B,H34C), C37(H37D,H37E,H37F), C28A(H28A,H28B,H28C), C27A(H27A,
 H27B,H27C), C27(H27D,H27E,H27F), C52(H52D,H52E,H52F), C52A(H52A,H52B,H52C),
 C16A(H16A,H16B,H16C), C28(H28D,H28E,H28F), C51(H51D,H51E,H51F), C15A(H15C,H15D,
 H15E), C22A(H22A,H22B,H22C), C0AA(H0AB,H0AC,H0AD), C22(H22D,H22E,H22F),
 C51A(H51A,H51B,H51C)
5.g Idealised tetrahedral OH refined as rotating group:
 O2(H2), O12A(H12A), O7(H7), O12(H12), O6A(H6AA)
;
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;