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- PDB-2v2g: Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Ar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v2g | ||||||
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Title | Crystal Structure of the C45S mutant of the Peroxiredoxin 6 of Arenicola Marina. Monoclinic form | ||||||
![]() | PEROXIREDOXIN 6 | ||||||
![]() | OXIDOREDUCTASE / PEROXIREDOXINS / ANTIOXIDANT ENZYMES / ARENICOLA MARINA | ||||||
Function / homology | ![]() peroxiredoxin activity / cell redox homeostasis / cellular response to oxidative stress / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Smeets, A. / Declercq, J.P. | ||||||
![]() | ![]() Title: The Crystal Structure of the C45S Mutant of Annelid Arenicola Marina Peroxiredoxin 6 Supports its Assignment to the Mechanistically Typical 2- Cys Subfamily without Any Formation of Toroid- Shaped Decamers. Authors: Smeets, A. / Loumaye, E. / Clippe, A. / Rees, J.F. / Knoops, B. / Declercq, J.P. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.9 KB | Display | ![]() |
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PDB format | ![]() | 161.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 445.3 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2v32C ![]() 2v41C ![]() 1hd2S ![]() 1nm3S ![]() 1prxS ![]() 1qmvS ![]() 1qq2S ![]() 1qxhS ![]() 1tp9S ![]() 1we0S ![]() 1x0rS ![]() 1xccS ![]() 1zyeS ![]() 2cv4S ![]() 2feg C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 25805.670 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-BEZ / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 45 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 45 TO SER ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: RESERVOIR : BIS-TRIS 0.1M PH 5.5, PEG3350 25%(W/V), DTT 0.001M, AMMONIUM SULFATE 0.1M DROP 1UL PROTEIN AND 1 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 1, 2006 / Details: TWO MIRRORS ARE USED FOR VERTICAL FOCUSSING |
Radiation | Monochromator: FIRST CRYSTAL FLAT AND N2 COOLED. SECOND ONE SAGITALLY BENT Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→14 Å / Num. obs: 131708 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SUPERPOSITION OF PDB ENTRIES 1HD2 1NM3 1PRX 1QMV 1QQ2 1QXH 1TP9 1WE0 1X0R 1XCC 1ZYE 2CV4 2FEG Resolution: 1.6→13.96 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.388 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.081 / 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: 20.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→13.96 Å
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Refine LS restraints |
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