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Yorodumi- PDB-4w8c: Crystal structure of the helical domain deleted form MsrA from Cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w8c | ||||||
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Title | Crystal structure of the helical domain deleted form MsrA from Clostridium oremlandii | ||||||
Components | Peptide methionine sulfoxide reductase MsrA | ||||||
Keywords | OXIDOREDUCTASE / MsrA / Clostridium oremlandii / truncated form | ||||||
Function / homology | Function and homology information L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein modification process Similarity search - Function | ||||||
Biological species | Alkaliphilus oremlandii OhILAs (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7568 Å | ||||||
Authors | Lee, E.H. / Hwang, K.Y. / Kim, H.-Y. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii Authors: Lee, E.H. / Lee, K. / Hwang, K.Y. / Kim, H.-Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w8c.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w8c.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 4w8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w8c_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 4w8c_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | 4w8c_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4w8c_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/4w8c ftp://data.pdbj.org/pub/pdb/validation_reports/w8/4w8c | HTTPS FTP |
-Related structure data
Related structure data | 4lwjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16503.271 Da / Num. of mol.: 2 / Fragment: UNP residues 1-144 / Mutation: U16C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkaliphilus oremlandii OhILAs (bacteria) Gene: msrA, Clos_1947 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) References: UniProt: A8MI53, 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: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 3.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2013 |
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→50 Å / Num. obs: 36941 / % possible obs: 96.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 26.65 Å2 / Net I/σ(I): 49.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LWJ Resolution: 1.7568→32.6 Å / FOM work R set: 0.7456 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 31.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.77 Å2 / Biso mean: 33.92 Å2 / Biso min: 11.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7568→32.6 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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