+Open data
-Basic information
Entry | Database: PDB / ID: 4g2e | ||||||
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Title | Crystal structure of a dimeric PrxQ from Sulfolobus tokodaii | ||||||
Components | Peroxiredoxin | ||||||
Keywords | OXIDOREDUCTASE / redox protein / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / dimer / A-type / LU / locally unfolded / peroxiredoxin / PrxQ / disulfide | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Perkins, A. / Gretes, M.C. / Karplus, P.A. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes. Authors: Perkins, A. / Gretes, M.C. / Nelson, K.J. / Poole, L.B. / Karplus, P.A. | ||||||
History |
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Remark 0 | THIS ENTRY 4G2E REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2YWNSF) ... THIS ENTRY 4G2E REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R2YWNSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 2YWN: A.EBIHARA, M.MANZOKU, Y.FUJIMOTO, S.YOKOYAMA, S.KURAMITSU, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g2e.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g2e.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4g2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/4g2e ftp://data.pdbj.org/pub/pdb/validation_reports/g2/4g2e | HTTPS FTP |
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-Related structure data
Related structure data | 4gqcC 4gqfC 2ywnS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17816.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: bcp4, STK_17850 / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: F9VNL8, peroxiredoxin |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.11 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2YWN. |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YWN Resolution: 1.4→26.615 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.9214 / SU ML: 0.12 / σ(F): 1.46 / Phase error: 14.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.266 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.03 Å2 / Biso mean: 19.8788 Å2 / Biso min: 7.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→26.615 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: 20
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