+Open data
-Basic information
Entry | Database: PDB / ID: 1oc3 | ||||||
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Title | HUMAN PEROXIREDOXIN 5 | ||||||
Components | PEROXIREDOXIN 5 | ||||||
Keywords | OXIDOREDUCTASE / ANTIOXIDANT ENZYME / PEROXIREDOXIN / THIOREDOXIN PEROXIDASE / THIOREDOXIN FOLD / PEROXISOME / MITOCHONDRION / TRANSIT PEPTIDE | ||||||
Function / homology | Function and homology information peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / NADPH oxidation / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / Detoxification of Reactive Oxygen Species / antioxidant activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / peroxidase activity / cellular response to reactive oxygen species / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / signaling receptor binding / intracellular membrane-bounded organelle / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Evrard, C. / Declercq, J.-P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structure of a Dimeric Oxidized Form of Human Peroxiredoxin 5 Authors: Evrard, C. / Capron, A. / Marchand, C. / Clippe, A. / Wattiez, R. / Soumillion, P. / Knoops, B. / Declercq, J.-P. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 A Resolution Authors: Declercq, J.P. / Evrard, C. / Clippe, A. / Stricht, D.V. / Bernard, A. / Knoops, B. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: A Twinned Monoclinic Crystal Form of Human Peroxiredoxin 5 with Eight Molecules in the Asymmetric Unit Authors: Declercq, J.P. / Evrard, C. #3: Journal: J.Biol.Chem. / Year: 1999 Title: Cloning and Characterization of Aoeb166, a Novel Mammalian Antioxidant Enzyme of the Peroxiredoxin Family Authors: Knoops, B. / Clippe, A. / Bogard, C. / Arsalane, K. / Wattiez, R. / Hermans, C. / Duconseille, E. / Falmagne, P. / Bernard, A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oc3.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oc3.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1oc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/1oc3 ftp://data.pdbj.org/pub/pdb/validation_reports/oc/1oc3 | HTTPS FTP |
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-Related structure data
Related structure data | 1hd2S 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 18193.850 Da / Num. of mol.: 3 / Fragment: PEROXIREDOXIN 5, RESIDUES 54-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P30044 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | REDUCES HYDROGEN PEROXIDE AND HYDROPEROX | |
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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: 2.89 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.3 Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.1 M SODIUM CITRATE BUFFER, PH 5.3, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 5.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8441 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2002 / Details: PREMIRROR, BENT MIRROR |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8441 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 38821 / % possible obs: 96.9 % / Redundancy: 4.2 % / Rsym value: 0.047 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.332 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. measured all: 164737 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 95.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HD2 Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.139 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.168 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2→72.55 Å
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