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Yorodumi- PDB-2jfp: Crystal structure of Enterococcus faecalis glutamate racemase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jfp | ||||||
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Title | Crystal structure of Enterococcus faecalis glutamate racemase in complex with D- Glutamate | ||||||
Components | GLUTAMATE RACEMASE | ||||||
Keywords | ISOMERASE / GLUTAMATE RACEMASE / PEPTIDOGLYCAN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / identical protein binding Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Lundqvist, T. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Exploitation of Structural and Regulatory Diversity in Glutamate Racemases Authors: Lundqvist, T. / Fisher, S.L. / Kern, G. / Folmer, R.H.A. / Xue, Y. / Newton, D.T. / Keating, T.A. / Alm, R.A. / De Jonge, B.L.M. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jfp.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jfp.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 2jfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jfp_validation.pdf.gz | 414.1 KB | Display | wwPDB validaton report |
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Full document | 2jfp_full_validation.pdf.gz | 424.4 KB | Display | |
Data in XML | 2jfp_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 2jfp_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/2jfp ftp://data.pdbj.org/pub/pdb/validation_reports/jf/2jfp | HTTPS FTP |
-Related structure data
Related structure data | 2jfnC 2jfoSC 2jfqC 2jfuC 2jfvC 2jfwC 2jfxC 2jfyC 2jfzC C: citing same article (ref.) 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: 31606.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q836J0, glutamate racemase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | DATABASE REFERENCE GENESEQP ADR04180 (PATENT DATABASE). CLOSEST PUBLIC REFERENCE IS GENPEPT NP_ ...DATABASE REFERENCE GENESEQP ADR04180 (PATENT DATABASE). CLOSEST PUBLIC REFERENCE IS GENPEPT NP_814851 HAS 2 DIFFERENCE | |
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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: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 7.5 Details: PROTEIN FORMULATED AT 10 MG/ML WITH 200MM AMMONIUM ACETATE PH 7.4, 5MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 0.1 M TRIS PH 7.5 0.2 MM CACL2 AND 20-25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.089 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.089 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→34 Å / Num. obs: 36578 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 1.98→2.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.5 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JFO Resolution: 1.98→34 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 46.1956 Å2 / ksol: 0.405976 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→34 Å
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Refine LS restraints |
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