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Yorodumi- PDB-3pil: Crystal structure of Mxr1 from Saccharomyces cerevisiae in reduce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pil | ||||||
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Title | Crystal structure of Mxr1 from Saccharomyces cerevisiae in reduced form | ||||||
Components | Peptide methionine sulfoxide reductase | ||||||
Keywords | OXIDOREDUCTASE / methionine-S-sulfoxide reductase | ||||||
Function / homology | Function and homology information 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 / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Ma, X.X. / Guo, P.C. / Shi, W.W. / Luo, M. / Tan, X.F. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural plasticity of the thioredoxin recognition site of yeast methionine S-sulfoxide reductase Mxr1 Authors: Ma, X.X. / Guo, P.C. / Shi, W.W. / Luo, M. / Tan, X.F. / Chen, Y. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pil.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pil.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pil_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 3pil_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 3pil_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 3pil_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/3pil ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pil | HTTPS FTP |
-Related structure data
Related structure data | 3pimC 3pinC 3bqeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21096.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MXR1 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) References: UniProt: P40029, peptide-methionine (S)-S-oxide reductase #2: Chemical | #3: 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: 1.98 Å3/Da / Density % sol: 37.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 4.6 Details: 0.2M ammonium acetate, 0.1M sodium acetate, 30% polyethylene glycol 4,000, pH 4.6, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→29.17 Å / Num. obs: 21889 / % possible obs: 98.4 % |
Reflection shell | Resolution: 2.03→2.14 Å / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BQE Resolution: 2.04→29.17 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.98 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→29.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.093 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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