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- PDB-2vd8: The crystal structure of alanine racemase from Bacillus anthracis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vd8 | ||||||
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Title | The crystal structure of alanine racemase from Bacillus anthracis (BA0252) | ||||||
![]() | ALANINE RACEMASE | ||||||
![]() | ISOMERASE / PYRIDOXAL 5'-PHOSPHATE / PEPTIDOGLYCAN SYNTHESIS / PLP / OPPF / L-ALANINE / D- ALANINE / PYRIDOXAL PHOSPHATE / STRUCTURAL GENOMICS / ALANINE RACEMASE / SPORE GERMINATION / OXFORD PROTEIN PRODUCTION FACILITY / STRUCTURAL PROTEOMICS IN EUROPE (SPINE) | ||||||
Function / homology | ![]() alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / pyridoxal phosphate binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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) | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.9 KB | Display | ![]() |
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PDB format | ![]() | 154.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.2 KB | Display | ![]() |
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Full document | ![]() | 497.5 KB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vd9C ![]() 1sftS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92556, 0.37705, 0.03412), Vector: |
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Components
#1: Protein | Mass: 44350.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PLP FORMS IMINO LINKAGE TO K41. ALL LYSINES DIMETHYLATED EXCEPT K41 AND K260 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q81VF6, UniProt: A0A6L7HC45*PLUS, alanine racemase #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 25% (W/V) POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.47→50 Å / Num. obs: 116056 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.47→1.52 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.2 / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SFT Resolution: 1.47→44.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.32 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.078 / 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: 10.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→44.19 Å
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Refine LS restraints |
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