+Open data
-Basic information
Entry | Database: PDB / ID: 4wr3 | ||||||
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Title | Y274F alanine racemase from E. coli | ||||||
Components | Alanine racemase, biosynthetic | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / peptidoglycan biosynthetic process / cell wall organization / pyridoxal phosphate binding / regulation of cell shape / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Squire, C.J. / Yosaatmadja, Y. / Patrick, W.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Mechanistic and Evolutionary Insights from the Reciprocal Promiscuity of Two Pyridoxal Phosphate-dependent Enzymes. Authors: Soo, V.W. / Yosaatmadja, Y. / Squire, C.J. / Patrick, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wr3.cif.gz | 286.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wr3.ent.gz | 231.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wr3_validation.pdf.gz | 492.1 KB | Display | wwPDB validaton report |
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Full document | 4wr3_full_validation.pdf.gz | 500.9 KB | Display | |
Data in XML | 4wr3_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 4wr3_validation.cif.gz | 74.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/4wr3 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/4wr3 | HTTPS FTP |
-Related structure data
Related structure data | 4itgC 4itxC 4xbjC 2rjgS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39185.879 Da / Num. of mol.: 4 / Mutation: Y274F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alr / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6B4, alanine racemase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 3.31 Å3/Da / Density % sol: 62.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 1.6 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 17, 2014 |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→19.72 Å / Num. obs: 168143 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.1 % / CC1/2: 0.998 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.86→1.9 Å / Redundancy: 16.4 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.632 / % possible all: 93.8 |
-Processing
Software | Name: REFMAC / Version: 5.8.0071 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RJG Resolution: 1.9→19.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.333 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.023 / 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: 22.793 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→19.72 Å
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