3UAO
Structure and Catalytic Mechanism of the Vitamin B3 Degradative Enzyme Maleamate Amidohydrolase from Bordetalla bronchiseptica RB50
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NBA | PDB ENTRY 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 295 | 0.2 M ammonium acetate, 0.1 M sodium cacodylate, 30% PEG-8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 157.56 | α = 90 |
b = 157.56 | β = 90 |
c = 198.48 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 120 | CCD | OXFORD RUBY CCD | mirrors | 2010-08-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 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 | 2.399 | 12.01 | 91.7 | 0.087 | 9.78 | 2.2 | 143682 | 131825 | 3 | 3 |
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 | 2.399 | 2.52 | 67.5 | 0.271 | 1.2 | 13186 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER | 2.399 | 12.01 | 143682 | 131825 | 1368 | 97.94 | 0.12796 | 0.12704 | 0.17252 | RANDOM | 14.739 |
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] | |
-0.63 | -0.63 | 1.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.656 |
r_dihedral_angle_4_deg | 16.457 |
r_dihedral_angle_3_deg | 16.308 |
r_dihedral_angle_1_deg | 10.077 |
r_scangle_it | 3.047 |
r_scbond_it | 1.891 |
r_angle_refined_deg | 1.626 |
r_mcangle_it | 1.136 |
r_angle_other_deg | 1.133 |
r_mcbond_it | 0.651 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11822 |
Nucleic Acid Atoms | |
Solvent Atoms | 576 |
Heterogen Atoms | 64 |
Software
Software | |
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Software Name | Purpose |
CrysalisPro | data collection |
PHASER | phasing |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |