+Open data
-Basic information
Entry | Database: PDB / ID: 2vl2 | ||||||
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Title | Oxidized and reduced forms of human peroxiredoxin 5 | ||||||
Components | (PEROXIREDOXIN-5) x 2 | ||||||
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: 1.925 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 | 2vl2.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vl2.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 2vl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vl2 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vl2 | HTTPS FTP |
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-Related structure data
Related structure data | 2vl3C 2vl9C 1hd2S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18209.850 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-162 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: Protein | | Mass: 18193.850 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-162 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 #3: Chemical | #4: 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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE |
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Crystal grow | pH: 8 / Details: NACL 0.1M TRIS PH 8 0.1M PEG 3350 20% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8156 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 7, 2005 / Details: MIRROR 2 BENT, VERTICALLY FOCUSSING |
Radiation | Monochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8156 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→57.5 Å / Num. obs: 42806 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 25.57 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.92→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HD2 Resolution: 1.925→57.5 Å / SU ML: 0.32 / Phase error: 25.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.32 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.925→57.5 Å
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Refine LS restraints |
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