Heterologous expression of an <i>in planta</i>-upregulated gene cluster in the wheat pathogen <i>Parastagonospora nodorum</i> establishes the biosynthesis of methylene-bridged depsides.
Nguyen, Hera T.; Sbaraini, Nicolau; Bracegirdle, Joe; Smithers, Luke; Moggach, Stephen A.; Vuong, Daniel; Lacey, Ernest; Solomon, Peter S.; Haywood, Joel; Piggott, Andrew M.; Chooi, Yit-Heng; Chemical science 16 (2025) 21852–21861; doi:10.1039/d5sc05442g

data_1576017
_publ_section_title
;
 Heterologous expression of an <i>in planta</i>-upregulated gene cluster
 in the wheat pathogen <i>Parastagonospora nodorum</i> establishes the
 biosynthesis of methylene-bridged depsides.
;
_journal_issue                   46
_journal_name_full               'Chemical science'
_journal_page_first              21852
_journal_page_last               21861
_journal_paper_doi               10.1039/d5sc05442g
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C19 H20 O8, 1[CH3OH]'
_chemical_formula_sum            'C20 H24 O9'
_chemical_formula_weight         408.39
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-05-28
_audit_creation_method
;
Olex2 1.5
(compiled 2025.04.05 svn.rf049d14d for OlexSys, GUI svn.r7224)
;
_audit_update_record
;
2025-07-16 deposited with the CCDC.	2025-10-14 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 104.606(9)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   16.6109(15)
_cell_length_b                   9.0434(5)
_cell_length_c                   25.320(2)
_cell_measurement_reflns_used    2396
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      44.2980
_cell_measurement_theta_min      5.4810
_cell_volume                     3680.6(5)
_computing_cell_refinement       'CrysAlisPro 1.171.43.143a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.143a 64-bit (release 25-10-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.143a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'XT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.997
_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     80.00 111.00   0.50   12.00    --   39.45  77.00 -90.00   62
  2  \w     -2.00  31.00   0.50   12.00    --   39.45 -99.00  30.00   66
  3  \w     30.00 107.00   0.50   12.00    --   39.45  38.00  60.00  154
  4  \w     11.00  37.00   0.50   12.00    --   39.45  89.00  14.38   52
  5  \w     17.00  58.00   0.50   12.00    --   39.45  77.00 -90.00   82
  6  \w     44.00  72.00   0.50   12.00    --   39.45 -99.00  30.00   56
  7  \w     72.00 112.00   0.50   12.00    --   39.45  38.00 -60.00   80
  8  \w     84.00 110.00   0.50   12.00    --   39.45 178.00  90.00   52
  9  \w    -27.00  26.00   0.50   12.00    --   39.45 -38.00   0.00  106
 10  \w     23.00  68.00   0.50   12.00    --   39.45 -99.00-180.00   90
 11  \w     11.00  39.00   0.50   12.00    --   39.45  92.00-149.20   56
 12  \w     27.00  87.00   0.50   12.00    --   39.45  38.00  30.00  120
 13  \w     21.00  54.00   0.50   12.00    --   39.45  69.00-175.17   66
 14  \w     76.00 111.00   0.50   12.00    --   39.45  69.00-175.17   70
 15  \w     26.00  52.00   0.50   12.00    --   39.45  57.00  90.00   52
 16  \w     55.00 103.00   0.50   12.00    --   39.45  57.00  90.00   96
 17  \w     30.00  68.00   0.50   12.00    --   39.45  38.00 -60.00   76
 18  \w     57.00 110.00   0.50   12.00    --   39.45 178.00 -60.00  106
 19  \w     29.00  65.00   0.50   12.00    --   39.45  38.00-180.00   72
 20  \w     70.00 108.00   0.50   12.00    --   39.45  38.00-180.00   76
 21  \w    -14.00  97.00   0.50   12.00    --   40.00   1.00  27.15  222
 22  \w     10.00  48.00   0.50   12.00    --   40.00 -47.00-117.71   76
 23  \w     11.00  38.00   0.50   12.00    --   40.00  90.00-110.95   54
 24  \w    -21.00   5.00   0.50   12.00    --   40.00 -47.00-117.71   52
 25  \w     69.00 112.00   0.50   12.00    --   40.00  -1.00-176.33   86
 26  \w     11.00  38.00   0.50   12.00    --   40.00  90.00 -25.96   54
 27  \w     22.00  51.00   0.50   12.00    --   40.00  -1.00-176.33   58
 28  \w    -31.00  -6.00   0.50   12.00    --   40.00  -1.00-176.33   50
 29  \w     12.00  41.00   0.50   12.00    --   40.00  89.00  96.90   58
 30  \w    -60.00   0.00   0.50   12.00    --  -41.95  77.00  60.00  120
 31  \w    -96.00 -27.50   0.50   12.00    --  -41.95 136.00-151.91  137
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
'XtaLAB Synergy, Single source at home/near, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0887895000
_diffrn_orient_matrix_UB_12      -0.0624019000
_diffrn_orient_matrix_UB_13      0.0206867000
_diffrn_orient_matrix_UB_21      -0.0179000000
_diffrn_orient_matrix_UB_22      -0.0369135000
_diffrn_orient_matrix_UB_23      0.0553568000
_diffrn_orient_matrix_UB_31      -0.0314305000
_diffrn_orient_matrix_UB_32      -0.1542028000
_diffrn_orient_matrix_UB_33      -0.0213425000
_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  0.0863
_diffrn_reflns_av_unetI/netI     0.0509
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            11019
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        44.623
_diffrn_reflns_theta_max         44.623
_diffrn_reflns_theta_min         3.608
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.989
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.65046
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.143a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_density_diffrn    1.474
_exptl_crystal_description       block
_exptl_crystal_F_000             1728
_exptl_crystal_size_max          0.071
_exptl_crystal_size_mid          0.042
_exptl_crystal_size_min          0.024
_refine_diff_density_max         0.457
_refine_diff_density_min         -0.309
_refine_diff_density_rms         0.070
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.179
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     252
_refine_ls_number_reflns         1467
_refine_ls_number_restraints     118
_refine_ls_restrained_S_all      1.141
_refine_ls_R_factor_all          0.1232
_refine_ls_R_factor_gt           0.1142
_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^)+(0.0179P)^2^+73.2389P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2107
_refine_ls_wR_factor_ref         0.2147
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1341
_reflns_number_total             1467
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc05442g2.cif
_cod_data_source_block           hcjf5
_cod_depositor_comments
'Adding full bibliography for 1576015--1576018.cif.'
_cod_database_code               1576017
_shelx_shelxl_version_number     2019/1
_chemical_oxdiff_formula         'C18 O10 H20'
_chemical_oxdiff_usercomment     'Hera sample for Heng'
_cell_oxdiff_angle_alpha         89.801(5)
_cell_oxdiff_angle_beta          104.602(6)
_cell_oxdiff_angle_gamma         89.930(5)
_cell_oxdiff_length_a            16.6022(13)
_cell_oxdiff_length_b            9.0439(4)
_cell_oxdiff_length_c            25.3263(17)
_cell_oxdiff_measurement_reflns_used 2397
_cell_oxdiff_volume              3679.8(4)
_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. Restrained distances
 O007-C00M \\sim O00L-C00M
 with sigma of 0.02
3. Rigid body (RIGU) restrains
 C008, C00A, C00B, C00C, C00D, C00F
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C00E, C00H, C00I, C00J, C00O, C00P
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C00N, C00S, C00R
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C00R, C00I, C00S, C00P, C00H, C00E, C00J, C00O, C00N
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C00Q, C00F, C00A, C00D, C008, C00C, C00B, C00K
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4.a Secondary CH2 refined with riding coordinates:
 C00K(H00A,H00B)
4.b Aromatic/amide H refined with riding coordinates:
 C00F(H00F)
4.c Tetrahedral OH refined with riding coordinates:
 O00L(H00L)
4.d Idealised Me refined as rotating group:
 C00N(H00C,H00D,H00E), C00Q(H00G,H00H,H00I), C00R(H00J,H00K,H00M), C00S(H00N,
 H00O,H00P)
4.e Idealised tetrahedral OH refined as rotating group:
 O001(H001), O003(H003), O005(H005), O006(H006)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 96 electrons were 
found in a volume of 360\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
1[CH3OH] per Asymmetric Unit 
which account for 144 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   0.9
_smtbx_masks_void_truncation_radius 1.0
_shelx_res_checksum              90803
_shelx_fab_checksum              73389
_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 1.484
_oxdiff_exptl_absorpt_empirical_full_min 0.600