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Yorodumi- PDB-2dy3: Crystal Structure of alanine racemase from Corynebacterium glutamicum -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dy3 | ||||||
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Title | Crystal Structure of alanine racemase from Corynebacterium glutamicum | ||||||
Components | Alanine racemase | ||||||
Keywords | ISOMERASE / alpha/beta barrel | ||||||
Function / homology | Function and homology information alanine racemase / D-alanine biosynthetic process / alanine racemase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Miyaguchi, I. / Sasaki, C. / Kato, R. / Oikawa, T. / Sugio, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Alanine Racemase from Corynebacterium glutamicum at 2.1 A resolution Authors: Miyaguchi, I. / Sasaki, C. / Kato, R. / Oikawa, T. / Sugio, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dy3.cif.gz | 280.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dy3.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 2dy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dy3_validation.pdf.gz | 486.6 KB | Display | wwPDB validaton report |
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Full document | 2dy3_full_validation.pdf.gz | 534.7 KB | Display | |
Data in XML | 2dy3_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 2dy3_validation.cif.gz | 86.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/2dy3 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/2dy3 | HTTPS FTP |
-Related structure data
Related structure data | 1bd0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39221.582 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: alr / Plasmid: pET3b, alarcCgl / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RSU9, alanine racemase #2: Chemical | ChemComp-PLP / #3: 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: 2.49 Å3/Da / Density % sol: 50.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: 20% PEG8000, 200mM ammonium sulfate, 100mM MES, pH 6.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 19, 2004 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.836 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 79817 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BD0 Resolution: 2.1→15 Å
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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