+Open data
-Basic information
Entry | Database: PDB / ID: 1urm | ||||||
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Title | HUMAN PEROXIREDOXIN 5, C47S MUTANT | ||||||
Components | PEROXIREDOXIN 5 | ||||||
Keywords | ANTIOXIDANT ENZYME / PEROXIREDOXIN / THIOREDOXIN PEROXIDASE / 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 / antioxidant activity ...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 / antioxidant activity / Detoxification of Reactive Oxygen Species / 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: 1.7 Å | ||||||
Authors | Declercq, J.P. / Evrard, C. | ||||||
Citation | Journal: J. Chem. Cryst. / Year: 2004 Title: Crystal Structure of the C47S Mutant of Human Peroxiredoxin 5 Authors: Evrard, C. / Smeets, A. / 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. / Vanderstricht, D. / 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1urm.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1urm.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1urm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/1urm ftp://data.pdbj.org/pub/pdb/validation_reports/ur/1urm | 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18177.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 54-214 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MUTATION CYS 47 SER IN COORDINATES / Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: P30044 | ||||||
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#2: Chemical | ChemComp-BEZ / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED MUTATION CYS 100 SER (FOLLOWING NUMBERING OF THE SWISSPROT DATABASE REFERENCE). FUNCTION ...ENGINEERED | Sequence details | C47S MUTANT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.5 % |
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Crystal grow | pH: 5.3 Details: PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE BUFFER PH 5.3, 0.2 M POTASSIUM SODIUM TARTRATE, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9911 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 12, 2001 / Details: BENT MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL FOCUSING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9911 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37 Å / Num. obs: 30149 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 32 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HD2 Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.189 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / 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: 15.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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