+Open data
-Basic information
Entry | Database: PDB / ID: 2wfc | ||||||
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Title | Crystal structure of peroxiredoxin 5 from Arenicola Marina | ||||||
Components | PEROXIREDOXIN 5 | ||||||
Keywords | OXIDOREDUCTASE / ANTIOXIDANT ENZYMES | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin / peroxisomal matrix / cell redox homeostasis / peroxidase activity Similarity search - Function | ||||||
Biological species | ARENICOLA MARINA (lugworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Smeets, A. / Declercq, J.P. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Peroxiredoxin 5 from Arenicola Marina Authors: Smeets, A. / Knoops, B. / Declercq, J.P. | ||||||
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 | 2wfc.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfc.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfc ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfc | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17516.062 Da / Num. of mol.: 4 / Fragment: RESIDUES 28-186 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARENICOLA MARINA (lugworm) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q1AN23, peroxiredoxin #2: Chemical | ChemComp-ACT / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 74 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 74 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: 1.98 Å3/Da / Density % sol: 38 % / Description: NONE |
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Crystal grow | Details: PEG 4000 29%(W/V), DTT 0.001 M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: ADSC CCD / Detector: CCD / Details: SECOND CRYSTAL SAGITALLY BENT |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→34.17 Å / Num. obs: 51140 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HD2 Resolution: 1.75→68.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.654 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→68.36 Å
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Refine LS restraints |
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