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Yorodumi- PDB-2vd9: The crystal structure of alanine racemase from Bacillus anthracis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vd9 | ||||||
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Title | The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P | ||||||
Components | ALANINE RACEMASE | ||||||
Keywords | ISOMERASE / PYRIDOXAL 5'-PHOSPHATE / PEPTIDOGLYCAN SYNTHESIS / PLP / OPPF / L-ALANINE / D-ALANINE / PYRIDOXAL PHOSPHATE / STRUCTURAL GENOMICS / ALANINE RACEMASE / SPORE GERMINATION / OXFORD PROTEIN PRODUCTION FACILITY (OPPF) / STRUCTURAL PROTEOMICS IN EUROPE (SPINE) | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS ANTHRACIS (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Au, K. / Ren, J. / Walter, T.S. / Harlos, K. / Nettleship, J.E. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M. / Oxford Protein Production Facility (OPPF) / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P). Authors: Au, K. / Ren, J. / Walter, T.S. / Harlos, K. / Nettleship, J.E. / Owens, R.J. / Stuart, D.I. / Esnouf, R.M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vd9.cif.gz | 189.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vd9.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/2vd9 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vd9 | HTTPS FTP |
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-Related structure data
Related structure data | 2vd8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.99662, 0.0821, 6.0E-5), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44350.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ALL LYSINES DIMETHYLATED EXCEPT K41 AND K260 / Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS References: UniProt: Q81VF6, UniProt: A0A6L7HC45*PLUS, alanine racemase |
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-Non-polymers , 5 types, 881 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 25% (W/V) POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS PH6.5, SOAKED IN 10MM L-ALA-P FOR 45 MINUTES, CRYOPROTECTED IN 25% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 48124 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VD8 Resolution: 2.1→45.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.555 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.64 Å
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Refine LS restraints |
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