+Open data
-Basic information
Entry | Database: PDB / ID: 1fva | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE METHIONINE SULFOXIDE REDUCTASE | ||||||
Components | PEPTIDE METHIONINE SULFOXIDE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Protein repair / L-methionine-(S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / cellular response to oxidative stress / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Lowther, W.T. / Brot, N. / Weissbach, H. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structure and mechanism of peptide methionine sulfoxide reductase, an "anti-oxidation" enzyme. Authors: Lowther, W.T. / Brot, N. / Weissbach, H. / Matthews, B.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Thiol-disulfide Exchange is Involved in the Catalytic Mechanism of Peptide Methionine Sulfoxide Reductase Authors: Lowther, W.T. / Brot, N. / Weissbach, H. / Honek, J.F. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fva.cif.gz | 93.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fva.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fva_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 1fva_full_validation.pdf.gz | 442.1 KB | Display | |
Data in XML | 1fva_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 1fva_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fva ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fva | HTTPS FTP |
-Related structure data
Related structure data | 1fvgSC S: Starting model for refinement C: citing same article (ref.) |
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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: 24032.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P54149, EC: 1.8.4.6 #2: 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: 2.3 Å3/Da / Density % sol: 46.44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: NaCl, DTT, 1,4 butanediol, PEG 8000, citrate, Na2HPO4, pH 4.7-7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.2 Å / Num. all: 158892 / Num. obs: 46997 / % possible obs: 97.7 % / Observed criterion σ(I): 3.5 / Redundancy: 3.4 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.225 / % possible all: 84 |
Reflection | *PLUS Num. measured all: 158892 |
Reflection shell | *PLUS % possible obs: 84 % / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fvg Resolution: 1.7→45.2 Å / σ(I): 3.5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 194.6 Å2 / ksol: 1.003 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→45.2 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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