+Open data
-Basic information
Entry | Database: PDB / ID: 1qmv | ||||||
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Title | thioredoxin peroxidase B from red blood cells | ||||||
Components | PEROXIREDOXIN-2 | ||||||
Keywords | OXIDOREDUCTASE / SULPHINIC ACID / THIOREDOXIN | ||||||
Function / homology | Function and homology information respiratory burst involved in inflammatory response / leukocyte activation / negative regulation of T cell differentiation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species ...respiratory burst involved in inflammatory response / leukocyte activation / negative regulation of T cell differentiation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / T cell homeostasis / antioxidant activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of blood coagulation / T cell proliferation / extrinsic apoptotic signaling pathway / removal of superoxide radicals / cell redox homeostasis / thymus development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / cellular response to oxidative stress / regulation of apoptotic process / response to oxidative stress / response to lipopolysaccharide / positive regulation of MAPK cascade / negative regulation of apoptotic process / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Isupov, M.N. / Littlechild, J.A. / Lebedev, A.A. / Errington, N. / Vagin, A.A. / Schroder, E. | ||||||
Citation | Journal: Structure / Year: 2000 Title: Crystal Structure of Decameric 2-Cys Peroxiredoxin from Human Erythrocytes at 1.7 A Resolution. Authors: Schroder, E. / Littlechild, J.A. / Lebedev, A.A. / Errington, N. / Vagin, A.A. / Isupov, M.N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallisation and Preliminary X-Ray Analysis of Human Thioredoxin Peroxidase B from Red Blood Cells Authors: Schroder, E. / Isupov, M.N. / Naran, A. / Littlechild, J.A. #2: Journal: Protein Sci. / Year: 1998 Title: Evidence that Peroxiredoxins are Novel Members of the Thioredoxin Fold Superfamily Authors: Schroder, E. / Ponting, C.P. #3: Journal: Biochim.Biophys.Acta / Year: 1998 Title: Porcine Natural Killer Enhancing Factor-B: Oligomerization and Identification as a Calpain Substrate in-Vitro Authors: Schroder, E. / Willis, A.C. / Ponting, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qmv.cif.gz | 426 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qmv.ent.gz | 352.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/1qmv ftp://data.pdbj.org/pub/pdb/validation_reports/qm/1qmv | HTTPS FTP |
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-Related structure data
Related structure data | 1prxS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 21862.715 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Details: PURIFIED FROM ONE MONTH OLD BLOOD / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Organ: BLOOD / References: UniProt: P32119, peroxiredoxin #2: 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: 2.4 Å3/Da / Density % sol: 49 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 16 % (V/V) PEG 400, 100 MM TRIS-HCL, PH 7.5, 10 % (V/V) 2-PROPANOL, 10 MM DITHIOERYTHREITOL | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 290 K / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | |||||||||||||||||||||||||||||||||||||||||||||
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: X11 / Wavelength: 0.9076 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9076 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 228010 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.057 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.493 / % possible all: 93.6 |
Reflection | *PLUS Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 93.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PRX Resolution: 1.7→20 Å / SU B: 2.67 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1106 / ESU R Free: 0.122
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Displacement parameters | Biso mean: 32.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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