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X-ray structure of the aminotransferase from Vibrio vulnificus responsible for the biosynthesis of 2,3-diacetamido-4-amino-2,3,4-trideoxy-arabinose in the presence of its external aldimine with 2,3-diacetamido-4-amino-2,3,4-trideoxy-l-arabinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 protein incubated with 5.0 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose and 1.0 mM PLP.
Precipitant: 15-20% (w/v) poly(ethylene glycol) 5000, 200 mM NaCl, and 100 mM MES (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.958 α = 83 b = 53.048 β = 82.17 c = 70.267 γ = 74.36
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 Bruker PHOTON II 2024-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.05 50 96.5 0.087 7.7 4.6 330200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.15 87.6 0.481 1.8 2.1
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 FOURIER SYNTHESIS THROUGHOUT 1.05 38.96 313419 16781 97.28 0.16028 0.15937 0.1709 0.17728 0.1844 RANDOM 8.476
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] 0.02 -0.02 -0.06 -0.03 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.976 r_dihedral_angle_2_deg 14.702 r_dihedral_angle_1_deg 6.456 r_rigid_bond_restr 4.787 r_long_range_B_refined 2.789 r_long_range_B_other 2.087 r_angle_refined_deg 1.663 r_scangle_other 1.304 r_scbond_it 0.99 r_scbond_other 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.976 r_dihedral_angle_2_deg 14.702 r_dihedral_angle_1_deg 6.456 r_rigid_bond_restr 4.787 r_long_range_B_refined 2.789 r_long_range_B_other 2.087 r_angle_refined_deg 1.663 r_scangle_other 1.304 r_scbond_it 0.99 r_scbond_other 0.99 r_mcangle_it 0.965 r_mcangle_other 0.965 r_mcbond_it 0.665 r_mcbond_other 0.665 r_angle_other_deg 0.528 r_chiral_restr 0.082 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5671 Nucleic Acid Atoms Solvent Atoms 956 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling REFMAC phasing