+Open data
-Basic information
Entry | Database: PDB / ID: 2vl9 | ||||||
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Title | Oxidized form of human peroxiredoxin 5 | ||||||
Components | PEROXIREDOXIN-5 | ||||||
Keywords | OXIDOREDUCTASE / THIOREDOXIN PEROXIDASE / ALTERNATIVE INITIATION / ANTIOXIDANT ENZYME / REDOX-ACTIVE CENTER / CYTOPLASM / PEROXIDASE / PEROXISOME / ANTIOXIDANT / POLYMORPHISM / MITOCHONDRION / PEROXIREDOXIN / TRANSIT PEPTIDE / THIOREDOXIN FOLD | ||||||
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: 2.7 Å | ||||||
Authors | Smeets, A. / Declercq, J.P. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2008 Title: The Crystal Structures of Oxidized Forms of Human Peroxiredoxin 5 with an Intramolecular Disulfide Bond Confirm the Proposed Enzymatic Mechanism for Atypical 2-Cys Peroxiredoxins. Authors: Smeets, A. / Marchand, C. / Linard, D. / Knoops, B. / Declercq, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vl9.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vl9.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vl9 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vl9 | HTTPS FTP |
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-Related structure data
Related structure data | 2vl2C 2vl3C 1oc3S 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: 18308.979 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-162 / Mutation: YES 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, peroxiredoxin #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 73 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 73 TO SER ...ENGINEERED | |
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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: 2.22 Å3/Da / Density % sol: 44.53 % Description: THE MODEL USED FOR THE MOLECULAR REPLACEMENT WAS A SIMULATION CREATED FROM PDB ENTRY 1OC3 |
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Crystal grow | pH: 6.5 Details: PEG 8000 20% SODIUM CACODYLATE 0.1 M PH 6.5 SODIUM ACETATE 0.1 M 6-AMINOCAPROIC ACID 3% W/V |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979764 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2005 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979764 Å / Relative weight: 1 |
Reflection twin | Operator: -K,H+K,L / Fraction: 0.479 |
Reflection | Resolution: 2.7→46 Å / Num. obs: 18076 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.05 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 4.05 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OC3 Resolution: 2.7→46 Å / Phase error: 24.5 / Stereochemistry target values: TWIN_LSQ_F Details: TWIN RATIO IS 50%. COMPUTED STRUCTURE FACTORS ARE NOT DIRECTLY COMPARABLE TO THE DEPOSITED OBSERVED STRUCTURE FACTORS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 170.46 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→46 Å
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Refine LS restraints |
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