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- PDB-2pvz: Crystal structure of methylaconitate isomerase PrpF from Shewanel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pvz | ||||||
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Title | Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis | ||||||
![]() | PrpF methylaconitate isomerase | ||||||
![]() | UNKNOWN FUNCTION / propionate catabolism / diaminopimelate epimerase like / aconitate binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garvey, G.S. / Rayment, I.R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.5 KB | Display | ![]() |
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PDB format | ![]() | 137.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 449.4 KB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 57 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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. |
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Components
#1: Protein | Mass: 41734.402 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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