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Yorodumi- PDB-6a2f: Crystal structure of biosynthetic alanine racemase from Pseudomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a2f | ||||||
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Title | Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa | ||||||
Components | Alanine racemase, biosynthetic | ||||||
Keywords | ISOMERASE / alanine racemase / Alr / Pseudomonas aeruginosa / L-alanine / D-alanine | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Dong, H. / Li, S. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2018 Title: Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1. Authors: Dong, H. / Han, Q. / Guo, Y. / Ju, J. / Wang, S. / Yuan, C. / Long, W. / He, X. / Xu, S. / Li, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a2f.cif.gz | 154 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a2f.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 6a2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/6a2f ftp://data.pdbj.org/pub/pdb/validation_reports/a2/6a2f | HTTPS FTP |
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-Related structure data
Related structure data | 1rcqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38582.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: alr, PA4930 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HUN4, alanine racemase #2: Chemical | #3: Chemical | #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: 2.88 Å3/Da / Density % sol: 57.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 4%(v/v) Tacsimate pH 4.0, 12%(w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 28844 / % possible obs: 90.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.5→2.64 Å / Rmerge(I) obs: 0.174 / Num. measured obs: 9785 / Num. unique obs: 2680 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rcq Resolution: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.723 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.59 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.04 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→50.01 Å
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Refine LS restraints |
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