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Crystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida in complex with sulfoquinovose substrate (sulfo-ED pathway)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P0DOV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Binary SQDH-SQ complex was obtained by soaking the sulfonate ligand on a crystal of apo_SQ grown using a 20 mg/mL protein solution in 50 mM TRIS buffer pH 7.5 containing 300 mM NaCl in a drop with 0.15 uL protein: 0.15 uL mother liquor, the latter comprising 0.1 M Magnesium formate dihydrate and 15% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 33.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.869 α = 90 b = 57.29 β = 93.12 c = 91.979 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2023-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 63.21 97.8 0.08 0.087 0.034 0.999 11.8 6.3 33364
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.5 0.764 0.839 0.343 0.815 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 48.66 31712 1645 97.76 0.22906 0.2265 0.2265 0.27845 0.2785 RANDOM 36.661
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -3.03 0.35 4.31 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.381 r_dihedral_angle_2_deg 10.131 r_long_range_B_refined 7.115 r_dihedral_angle_1_deg 6.536 r_mcangle_it 4.852 r_scbond_it 4.647 r_mcbond_it 3.753 r_angle_refined_deg 1.71 r_chiral_restr 0.112 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.381 r_dihedral_angle_2_deg 10.131 r_long_range_B_refined 7.115 r_dihedral_angle_1_deg 6.536 r_mcangle_it 4.852 r_scbond_it 4.647 r_mcbond_it 3.753 r_angle_refined_deg 1.71 r_chiral_restr 0.112 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3674 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction BALBES phasing