9BGR
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
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 9BGP |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.24 | 45.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.958 | α = 83 |
b = 53.048 | β = 82.17 |
c = 70.267 | γ = 74.36 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER D8 QUEST | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.17728 | RANDOM | 8.476 |
Temperature Factor Modeling | ||||||
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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 | |
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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 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5671 |
Nucleic Acid Atoms | |
Solvent Atoms | 956 |
Heterogen Atoms | 204 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |
REFMAC | phasing |