+Open data
-Basic information
Entry | Database: PDB / ID: 4bhy | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of alanine racemase from Aeromonas hydrophila | ||||||
Components | ALANINE RACEMASE | ||||||
Keywords | ISOMERASE / D-AMINO ACIDS | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | AEROMONAS HYDROPHILA SUBSP. HYDROPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Otero, L.H. / Carrasco-Lopez, C. / Bernardo-Garcia, N. / Hermoso, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural Basis for the Broad Specificity of a New Family of Amino-Acid Racemases. Authors: Espaillat, A. / Carrasco-Lopez, C. / Bernardo-Garcia, N. / Pietrosemoli, N. / Otero, L.H. / Alvarez, L. / De Pedro, M.A. / Pazos, F. / Davis, B.M. / Waldor, M.K. / Hermoso, J.A. / Cava, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bhy.cif.gz | 518 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bhy.ent.gz | 430.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bhy_validation.pdf.gz | 447 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bhy_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 4bhy_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 4bhy_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/4bhy ftp://data.pdbj.org/pub/pdb/validation_reports/bh/4bhy | HTTPS FTP |
-Related structure data
Related structure data | 4beqC 4beuC 4bf5C 1rcqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41504.527 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AEROMONAS HYDROPHILA SUBSP. HYDROPHILA (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0KH11, alanine racemase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 47.77 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97901 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97901 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→48.04 Å / Num. obs: 21300 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 97.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 95.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RCQ Resolution: 3.25→47.32 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.8234 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.656 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. DISORDERED REGIONS WERE NOT MODELED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.88 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.837 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→47.32 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.25→3.41 Å / Total num. of bins used: 11
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|