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Open data
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Basic information
Entry | Database: PDB / ID: 2xih | ||||||
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Title | The structure of ascorbate peroxidase Compound III | ||||||
![]() | ASCORBATE PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / FERRYL ION / FERROUS HEME | ||||||
Function / homology | ![]() L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gumiero, A. / Raven, E.L. / Moody, P.C.E. | ||||||
![]() | ![]() Title: Nature of the ferryl heme in compounds I and II. Authors: Gumiero, A. / Metcalfe, C.L. / Pearson, A.R. / Raven, E.L. / Moody, P.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 815.5 KB | Display | ![]() |
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Full document | ![]() | 821.8 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xi6C ![]() 2xifC ![]() 2xilC ![]() 2xj5C ![]() 2xj6C ![]() 2xj8C ![]() 1oafS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26956.373 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-250 Source method: isolated from a genetically manipulated source Details: COMPOUND I FORMED BY PHOTOREDUCTION OF COMPOUND III Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 483 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-K / |
#5: Chemical | ChemComp-OXY / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 8.3 / Details: LISO4 2.25M, HEPES 0.1M, PH8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6 Å / Relative weight: 1 |
Reflection | Resolution: 1.485→1.69 Å / Num. obs: 35606 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.485→1.524 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.11 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OAF Resolution: 1.65→35.99 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.083 / 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: 23.785 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→35.99 Å
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Refine LS restraints |
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