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Yorodumi- PDB-3hvv: Escherichia coli Thiol peroxidase (Tpx) peroxidatic cysteine to s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hvv | ||||||
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Title | Escherichia coli Thiol peroxidase (Tpx) peroxidatic cysteine to serine mutant (C61S) | ||||||
Components | Thiol peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Tpx / peroxiredoxin / peroxidase / Antioxidant | ||||||
Function / homology | Function and homology information hydroperoxide reductase activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress / periplasmic space / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Hall, A. / Sankaran, B. / Karplus, P.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural changes common to catalysis in the Tpx peroxiredoxin subfamily. Authors: Hall, A. / Sankaran, B. / Poole, L.B. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hvv.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hvv.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/3hvv ftp://data.pdbj.org/pub/pdb/validation_reports/hv/3hvv | HTTPS FTP |
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-Related structure data
Related structure data | 3hvsSC 3hvxC 3i43C 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
#1: Protein | Mass: 17700.953 Da / Num. of mol.: 1 / Mutation: C61S Source method: isolated from a genetically manipulated source Details: See Baker and Poole, 2003. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 (XL-1 Blue) / Gene: b1324, JW1317, tpx, yzzJ / Plasmid: pPROK1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: P0A862, peroxiredoxin |
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#2: 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: 2.12 Å3/Da / Density % sol: 41.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 22% (w/v) PEG 8000, 0.05 M potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2008 |
Radiation | Monochromator: Single crystal, cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→42 Å / Num. obs: 13755 / % possible obs: 92.8 % / Redundancy: 7.7 % / Rsym value: 0.056 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1403 / Rsym value: 0.457 / % possible all: 63.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: chain A of pdb entry 3HVS Resolution: 1.75→42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.667 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.12 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.581 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.796 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -19.408 Å / Origin y: 5.644 Å / Origin z: 6.295 Å
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