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Yorodumi- PDB-1fvg: CRYSTAL STRUCTURE OF BOVINE PEPTIDE METHIONINE SULFOXIDE REDUCTASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fvg | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE PEPTIDE 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 / MAD / Resolution: 1.6 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 | 1fvg.cif.gz | 50.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fvg.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fvg_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 1fvg_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 1fvg_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1fvg_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fvg ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fvg | HTTPS FTP |
-Related 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: 22385.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DITHIOTHREITOL COMPLEX / Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: P54149, EC: 1.8.4.6 |
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#2: Chemical | ChemComp-DTT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.55 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: dithiothreitol, PEG 8000, citrate, Na2HPO4, dimethyl sulfoxide, NaCl, pH 4.70, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: 0.9787,0.9788,0.9537 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→53.5 Å / Num. all: 86018 / Num. obs: 23472 / % possible obs: 95.8 % / Observed criterion σ(I): 8 / Redundancy: 4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 37.2 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.171 / % possible all: 93.9 | ||||||||||||
Reflection | *PLUS Num. measured all: 86018 | ||||||||||||
Reflection shell | *PLUS % possible obs: 93.9 % / Mean I/σ(I) obs: 8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→53.58 Å / σ(I): 8 / Stereochemistry target values: Engh & Huber Details: The structure factors represent the "optimized" reference structure factors (Fpsha) from a three wavelength MAD experiment analyzed by SHARP.
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Solvent computation | Bsol: 141.2 Å2 / ksol: 0.802 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→53.58 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / % reflection Rfree: 10 % / Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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