Genome mining reveals a highly oxidized bacterial perhydrophenanthrene meroterpenoid smelanic acid.
Yang, Ziyi; Pan, Xingming; Deng, Lianchun; Wang, Zengyuan; Li, Fang-Ru; Lin, Xiaoxu; Xu, Hui-Min; Dong, Liao-Bin; Organic & biomolecular chemistry 23 (2025) 7773–7779; doi:10.1039/d5ob01195g

data_7160665
_publ_section_title
;
 Genome mining reveals a highly oxidized bacterial perhydrophenanthrene
 meroterpenoid smelanic acid.
;
_journal_issue                   34
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              7773
_journal_page_last               7779
_journal_paper_doi               10.1039/d5ob01195g
_journal_volume                  23
_journal_year                    2025
_chemical_absolute_configuration rm
_chemical_formula_moiety         'C23 H34 O5'
_chemical_formula_sum            'C23 H34 O5'
_chemical_formula_weight         390.50
_space_group_crystal_system      tetragonal
_space_group_IT_number           76
_space_group_name_Hall           'P 4w'
_space_group_name_H-M_alt        'P 41'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-03-06
_audit_creation_method
;
Olex2 1.5-ac5-024
(compiled 2022.04.12 svn.rca3783a0 for Rigaku Oxford Diffraction, GUI svn.r6498)
;
_audit_update_record
;
2025-05-18 deposited with the CCDC.	2025-08-08 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   18.0532(5)
_cell_length_b                   18.0532(5)
_cell_length_c                   6.4334(2)
_cell_measurement_reflns_used    2852
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      69.9930
_cell_measurement_theta_min      2.4520
_cell_volume                     2096.76(10)
_computing_cell_refinement       'CrysAlisPro 1.171.42.94a (Rigaku OD, 2023)'
_computing_data_collection       'CrysAlisPro 1.171.42.94a (Rigaku OD, 2023)'
_computing_data_reduction        'CrysAlisPro 1.171.42.94a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5-ac5-024 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac5-024 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      150.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.980
_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     43.00  70.00   0.50    0.65    --    0.00-156.00 -80.00   54
  2  \w   -134.00-103.00   0.50    2.60    --  -55.51-105.00 -23.00   62
  3  \w    -20.00   6.00   0.50    2.60    --  -55.51  22.00 -45.00   52
  4  \w     16.00 109.00   0.50    2.60    --   55.51-120.00  76.00  186
  5  \w   -169.00-113.00   0.50    2.60    -- -103.00-105.00 -23.00  112
  6  \w   -169.00-143.00   0.50    2.60    -- -103.00 -22.00 148.00   52
  7  \w   -125.00 -99.00   0.50    2.60    -- -103.00 -22.00 148.00   52
  8  \w     35.00  61.00   0.50    2.60    --  111.01  22.00 -45.00   52
  9  \w     44.00  99.00   0.50    2.60    --  111.01-105.00 -23.00  110
 10  \w     97.00 123.00   0.50    2.60    --  111.01 156.00 -43.00   52
 11  \w     36.00  62.00   0.50    0.65    --    0.00  19.00 -30.00   52
 12  \w    -64.00 -31.00   0.50    0.65    --    0.00 156.00 -43.00   66
 13  \w    -25.00  25.00   0.50    2.60    --  -55.51  30.00-180.00  100
 14  \w    -32.00  -4.00   0.50    2.60    --  -55.51  30.00  30.00   56
 15  \w    -10.00  16.00   0.50    2.60    --  -55.51  15.00 150.00   52
 16  \w    -24.00  27.00   0.50    2.60    --  -55.51  30.00   0.00  102
 17  \w    -54.00 -22.00   0.50    2.60    -- -103.00  50.00-150.00   64
 18  \w    -53.00 -22.00   0.50    2.60    -- -103.00  50.00-180.00   62
 19  \w    -73.00 -23.00   0.50    2.60    -- -103.00  64.00 -30.00  100
 20  \w    -54.00 -29.00   0.50    2.60    -- -103.00  50.00  30.00   50
 21  \w    -98.00 -64.00   0.50    2.60    -- -103.00  77.00 150.00   68
 22  \w     18.00  68.00   0.50    2.60    --  111.01 -77.00  60.00  100
 23  \w     49.00 108.00   0.50    2.60    --  111.01-112.00 -90.00  118
 24  \w     24.00  78.00   0.50    2.60    --  111.01 -64.00 120.00  108
 25  \w     23.00  76.00   0.50    2.60    --  111.01 -64.00  90.00  106
 26  \w     50.00  79.00   0.50    2.60    --  111.01 -64.00-120.00   58
 27  \w     27.00  58.00   0.50    2.60    --  111.01 -50.00 -60.00   62
 28  \w     30.00  56.00   0.50    2.60    --  111.01 -50.00-150.00   52
 29  \w     81.00 106.00   0.50    2.60    --  111.01 -77.00  60.00   50
 30  \w     31.00  56.00   0.50    2.60    --  111.01 -50.00 -30.00   50
 31  \w     83.00 174.00   0.50    2.60    --  111.01 120.00 159.00  182
 32  \w     84.00 115.00   0.50    2.60    --  111.01  22.00 -45.00   62
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0152367000
_diffrn_orient_matrix_UB_12      -0.0736224000
_diffrn_orient_matrix_UB_13      0.1132519000
_diffrn_orient_matrix_UB_21      0.0190108000
_diffrn_orient_matrix_UB_22      -0.0369545000
_diffrn_orient_matrix_UB_23      -0.2091385000
_diffrn_orient_matrix_UB_31      0.0818135000
_diffrn_orient_matrix_UB_32      0.0222336000
_diffrn_orient_matrix_UB_33      0.0274298000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0431
_diffrn_reflns_av_unetI/netI     0.0519
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.980
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -22
_diffrn_reflns_limit_l_max       7
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            8743
_diffrn_reflns_point_group_measured_fraction_full 0.987
_diffrn_reflns_point_group_measured_fraction_max 0.961
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         71.124
_diffrn_reflns_theta_min         2.447
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.689
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.48591
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.94a (Rigaku Oxford Diffraction, 2023)
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    1.237
_exptl_crystal_description       irregular
_exptl_crystal_F_000             848
_exptl_crystal_size_max          0.37
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.01
_refine_diff_density_max         0.262
_refine_diff_density_min         -0.219
_refine_diff_density_rms         0.052
_refine_ls_abs_structure_details
;
 Flack x determined using 1225 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.01(17)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.110
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     260
_refine_ls_number_reflns         3902
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.110
_refine_ls_R_factor_all          0.0732
_refine_ls_R_factor_gt           0.0612
_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^)+(0.0758P)^2^+0.8017P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1472
_refine_ls_wR_factor_ref         0.1534
_reflns_Friedel_coverage         0.790
_reflns_Friedel_fraction_full    0.978
_reflns_Friedel_fraction_max     0.937
_reflns_number_gt                3400
_reflns_number_total             3902
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ob01195g2.cif
_cod_data_source_block           390y2y_auto
_cod_depositor_comments          'Adding full bibliography for 7160665.cif.'
_cod_original_cell_volume        2096.76(13)
_cod_database_code               7160665
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H O '
_shelx_estimated_absorpt_t_max   0.993
_shelx_estimated_absorpt_t_min   0.785
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2.a Ternary CH refined with riding coordinates:
 C2(H2), C17(H17), C16(H16), C18(H18), C14(H14)
2.b Secondary CH2 refined with riding coordinates:
 C4(H4A,H4B), C7(H7A,H7B), C13(H13A,H13B), C3(H3A,H3B), C8(H8A,H8B), C12(H12A,
 H12B)
2.c Idealised Me refined as rotating group:
 C24(H24A,H24B,H24C), C28(H28A,H28B,H28C), C27(H27A,H27B,H27C), C25(H25A,H25B,
 H25C), C26(H26A,H26B,H26C)
2.d Idealised tetrahedral OH refined as rotating group:
 O20(H20), O22(H22)
;
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 2.612
_oxdiff_exptl_absorpt_empirical_full_min 0.535