Production of Antitubercular Depsipeptides via Biosynthetic Engineering of Cinnamoyl Units
Yang, Zhijie; Sun, Changli; Liu, Zhiyong; Liu, Qing; Zhang, Tianyu; Ju, Jianhua; Ma, Junying; Journal of Natural Products  (2020) –; doi:10.1021/acs.jnatprod.0c00194

data_1557921
_publ_section_title
;
 Production of Antitubercular Depsipeptides via Biosynthetic Engineering
 of Cinnamoyl Units
;
_journal_name_full               'Journal of Natural Products'
_journal_paper_doi               10.1021/acs.jnatprod.0c00194
_journal_year                    2020
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C70 H86 N12 O16'
_chemical_formula_sum            'C70 H86 N12 O16'
_chemical_formula_weight         1351.50
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_audit_creation_date             2020-02-22
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 104.4750(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   12.62640(10)
_cell_length_b                   21.0187(2)
_cell_length_c                   15.18750(10)
_cell_measurement_reflns_used    23697
_cell_measurement_temperature    100(1)
_cell_measurement_theta_max      72.6860
_cell_measurement_theta_min      4.0620
_cell_volume                     3902.67(6)
_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(1)
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.987
_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    -32.00  33.00   0.50    1.00    --    0.00 -82.00  30.00  130
  2  \w    -30.00  33.00   0.50    1.00    --    0.00 -77.00  90.00  126
  3  \w    -27.00  33.00   0.50    1.00    --    0.00 -82.00 -90.00  120
  4  \w     30.00  89.00   0.50    1.00    --    0.00  57.00 -30.00  118
  5  \w    -32.00  36.00   0.50    1.00    --    0.00 -82.00 -30.00  136
  6  \w    -12.00  34.00   0.50    1.00    --    0.00 -82.00 150.00   92
  7  \w    -23.00   2.00   0.50    1.00    --    0.00 -82.00 -60.00   50
  8  \w      8.00  64.00   0.50    6.00    --   97.60 -61.00-150.00  112
  9  \w    111.00 137.00   0.50    6.00    --   97.60  61.00-120.00   52
 10  \w     68.00 101.00   0.50    6.00    --   97.60  61.00-120.00   66
 11  \w     71.00 138.00   0.50    6.00    --   97.60  45.00 -30.00  134
 12  \w      9.00  98.00   0.50    6.00    --   97.60 -82.00  30.00  178
 13  \w     20.00  49.00   0.50    6.00    --   97.60 -82.00-150.00   58
 14  \w     53.00 109.00   0.50    6.00    --   97.60 -82.00-150.00  112
 15  \w     44.00 127.00   0.50    6.00    --   97.60 -61.00  60.00  166
 16  \w     42.00 133.00   0.50    6.00    --   97.60 -82.00  60.00  182
 17  \w     99.00 154.00   0.50    6.00    --   97.60  82.00-150.00  110
 18  \w     88.00 127.00   0.50    6.00    --   97.60 -82.00 120.00   78
 19  \w     12.00 103.00   0.50    6.00    --   97.60 -82.00 -90.00  182
 20  \w     96.00 154.00   0.50    6.00    --   97.60  82.00   0.00  116
 21  \w     21.00  47.00   0.50    6.00    --   97.60 -82.00-180.00   52
 22  \w     87.00 112.00   0.50    6.00    --   97.60 -82.00-180.00   50
 23  \w     86.00 121.00   0.50    6.00    --   97.60 -61.00-150.00   70
 24  \w     67.00 187.00   0.50    6.00    --   97.60  30.00  90.00  240
 25  \w     11.00 145.00   0.50    6.00    --   97.60 -15.00  30.00  268
 26  \w     64.00 174.00   0.50    6.00    --   97.60  74.00-162.41  220
;
_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  0.0346
_diffrn_reflns_av_unetI/netI     0.0402
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.987
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       26
_diffrn_reflns_limit_k_min       -25
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            41404
_diffrn_reflns_point_group_measured_fraction_full 0.992
_diffrn_reflns_point_group_measured_fraction_max 0.967
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.172
_diffrn_reflns_theta_min         3.615
_exptl_absorpt_coefficient_mu    0.681
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.95242
_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 colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.150
_exptl_crystal_description       plate
_exptl_crystal_F_000             1436
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.383
_refine_diff_density_min         -0.377
_refine_diff_density_rms         0.042
_refine_ls_abs_structure_details
;
 Flack x determined using 5816 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.10(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.063
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     892
_refine_ls_number_reflns         15144
_refine_ls_number_restraints     15
_refine_ls_restrained_S_all      1.077
_refine_ls_R_factor_all          0.0638
_refine_ls_R_factor_gt           0.0511
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0947P)^2^+0.4651P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1415
_refine_ls_wR_factor_ref         0.1478
_reflns_Friedel_coverage         0.906
_reflns_Friedel_fraction_full    0.986
_reflns_Friedel_fraction_max     0.947
_reflns_number_gt                13635
_reflns_number_total             15144
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np0c00194_si_003.cif
_cod_data_source_block           yangzhijie_b_collect
_cod_database_code               1557921
_shelx_shelxl_version_number     2016/6
_shelx_estimated_absorpt_t_max   0.967
_shelx_estimated_absorpt_t_min   0.935
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Rigid bond restraints
 N4, C26
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 C25, N4
 with sigma for 1-2 distances of 0.0002 and sigma for 1-3 distances of 0.0001
 C71
 with sigma for 1-2 distances of 0.0001 and sigma for 1-3 distances of 0.0001
3. Uiso/Uaniso restraints and constraints
Uanis(C62) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C71) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
4.a Ternary CH refined with riding coordinates:
 C16(H16), C47(H47), C39(H39), C23(H23), C17(H17), C34(H34), C65(H65),
 C38(H38), C20(H20), C52(H52), C59(H59), C53(H53), C61(H61)
4.b Secondary CH2 refined with riding coordinates:
 C50(H50A,H50B), C35(H35A,H35B), C21(H21A,H21B), C24(H24A,H24B), C66(H66A,
 H66B), C49(H49A,H49B), C48(H48A,H48B), C57(H57A,H57B), C60(H60A,H60B)
4.c Aromatic/amide H refined with riding coordinates:
 N1(H1), N2(H2), N5(H5), N7(H7), N9(H9), N3(H3), C26(H26), N12(H12), C3(H3A),
 N11(H11), N4(H4), C2(H2A), N10(H10A), C31(H31), C68(H68), C29(H29), C28(H28),
 C6(H6), C8(H8), C45(H45), C30(H30), C7(H7A), C5(H5B), C69(H69), C41(H41),
 C44(H44), C42(H42), C10(H10B), C72(H72), C43(H43), C11(H11A), C71(H71)
4.d X=CH2 refined with riding coordinates:
 N6(H6A,H6B)
4.e Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C54(H54A,H54B,H54C), C55(H55A,H55B,H55C), C12(H12A,H12B,
 H12C), C63(H63A,H63B,H63C), C62(H62A,H62B,H62C)
4.f Idealised tetrahedral OH refined as rotating group:
 O10(H10), O5(H5A), O16(H16A)
;
_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
;