+Open data
-Basic information
Entry | Database: PDB / ID: 4xbj | ||||||
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Title | Y274F alanine racemase from E. coli inhibited by l-ala-p | ||||||
Components | Alanine racemase, biosynthetic | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
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: 2.25 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 | 4xbj.cif.gz | 278.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbj.ent.gz | 225.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbj ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbj | HTTPS FTP |
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-Related structure data
Related structure data | 4itgC 4itxC 4wr3SC 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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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 | #3: Chemical | ChemComp-SO4 / #4: 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: 3.3 Å3/Da / Density % sol: 62.71 % |
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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: Nov 28, 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 twin |
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Reflection | Resolution: 2.25→19.91 Å / Num. obs: 95615 / % possible obs: 99.7 % / Redundancy: 11.4 % / CC1/2: 0.992 / Rpim(I) all: 0.088 / Net I/σ(I): 10.7 | |||||||||||||||
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 2 / CC1/2: 0.617 / Rpim(I) all: 0.432 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WR3 Resolution: 2.25→19.9 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.051 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.034 / 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: 21.717 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→19.9 Å
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