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Yorodumi- PDB-2pvz: Crystal structure of methylaconitate isomerase PrpF from Shewanel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pvz | ||||||
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Title | Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis | ||||||
Components | PrpF methylaconitate isomerase | ||||||
Keywords | UNKNOWN FUNCTION / propionate catabolism / diaminopimelate epimerase like / aconitate binding | ||||||
Function / homology | Function and homology information intramolecular oxidoreductase activity, transposing C=C bonds / propionate catabolic process, 2-methylcitrate cycle / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds Similarity search - Function | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Garvey, G.S. / Rayment, I.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function. Authors: Garvey, G.S. / Rocco, C.J. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pvz.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pvz.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/2pvz ftp://data.pdbj.org/pub/pdb/validation_reports/pv/2pvz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer. There is one homodimer in the asymetric unit. |
-Components
#1: Protein | Mass: 41734.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: PrpF / Plasmid: pPRP196 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8EJW4 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EDO / #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: 2.45 Å3/Da / Density % sol: 49.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 300-350 mM NaCl, 21-24% methyl ether poly(ethylene glycol) 5000, buffered with 100 mM triethanolamine (pH 8.0 at 25 C). , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.964108 Å |
Detector | Detector: CCD / Date: Apr 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964108 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→75.81 Å / Num. obs: 204015 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 9.1 / Num. unique all: 3643 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→75.81 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.669 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.133 / 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: 14.034 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→75.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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