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Yorodumi- PDB-1qxh: Crystal Structure of Escherichia coli Thiol Peroxidase in the Oxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qxh | ||||||
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Title | Crystal Structure of Escherichia coli Thiol Peroxidase in the Oxidized State | ||||||
Components | Thiol peroxidase | ||||||
Keywords | OXIDOREDUCTASE / thiol peroxidase / scavengase P20 / antioxidant enzyme / peroxiredoxin | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å | ||||||
Authors | Choi, J. / Choi, S. / Choi, J. / Shin, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of Escherichia coli thiol peroxidase in the oxidized state: insights into intramolecular disulfide formation and substrate binding in atypical 2-Cys peroxiredoxins Authors: Choi, J. / Choi, S. / Choi, J. / Cha, M.-K. / Kim, I.-H. / Shin, W. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Crystallization and preliminary X-ray analysis of Escherichia coli p20, a novel thiol peroxidase Authors: Choi, J. / Choi, S. / Choi, J. / Cha, M.-K. / Kim, I.-H. / Shin, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qxh.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qxh.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/1qxh ftp://data.pdbj.org/pub/pdb/validation_reports/qx/1qxh | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17717.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: P0A862, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: 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: 1.85 Å3/Da / Density % sol: 33.01 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, iso-propyl alcohol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 8, 2002 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 15120 / Num. obs: 15120 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 8.5 / Num. unique all: 1429 / Rsym value: 0.21 / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 51963 |
Reflection shell | *PLUS % possible obs: 99.4 % / Num. unique obs: 1429 / Num. measured obs: 4891 / Rmerge(I) obs: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.2→20.02 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 930183.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.5007 Å2 / ksol: 0.332231 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.188 / Rfactor Rfree: 0.246 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.28 |