+Open data
-Basic information
Entry | Database: PDB / ID: 4k7i | ||||||
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Title | HUMAN PEROXIREDOXIN 5 with a fragment | ||||||
Components | Peroxiredoxin-5, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / enzyme / cytosol | ||||||
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 / cellular response to reactive oxygen species / peroxidase activity / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Guichou, J.F. | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Comparing Binding Modes of Analogous Fragments Using NMR in Fragment-Based Drug Design: Application to PRDX5 Authors: Aguirre, C. / Brink, T.T. / Guichou, J.F. / Cala, O. / Krimm, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k7i.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k7i.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k7i_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 4k7i_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 4k7i_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 4k7i_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k7i ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k7i | HTTPS FTP |
-Related structure data
Related structure data | 4k7nC 4k7oC 4mmmC 1hd2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17835.475 Da / Num. of mol.: 3 / Fragment: catalytic domain, UNP residues 54-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDX5, ACR1, SBBI10 / Production host: Escherichia coli (E. coli) / References: UniProt: P30044, peroxiredoxin #2: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 22% PEG3350, 0.1M sodium citrate buffer, 0.2M potassium sodium tartrate, 5mM 1,4-dithio-dl-threitol, 0.02%(w/v) sodium azide, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2012 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→47.6 Å / Num. all: 29176 / Num. obs: 28855 / % possible obs: 98.9 % / Observed criterion σ(F): 5.3 / Observed criterion σ(I): 2.1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 2.25→47.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 5.3 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HD2 Resolution: 2.25→47.6 Å / Cross valid method: THROUGHOUT / σ(F): 2.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 27.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→47.6 Å
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