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Open data
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Basic information
Entry | Database: PDB / ID: 7vn0 | ||||||
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Title | CATPO mutant - T188A | ||||||
![]() | Catalase | ||||||
![]() | OXIDOREDUCTASE / catalase / phenol oxidase / lateral channel / mutant | ||||||
Function / homology | ![]() catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Yuzugullu Karakus, Y. / Balci Unver, S. / Zengin Karatas, M. / Goc, G. / Pearson, A.R. / Yorke, B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Investigation of how gate residues in the main channel affect the catalytic activity of Scytalidium thermophilum catalase. Authors: Yuzugullu Karakus, Y. / Goc, G. / Zengin Karatas, M. / Balci Unver, S. / Yorke, B.A. / Pearson, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 586.1 KB | Display | ![]() |
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PDB format | ![]() | 477.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 110.5 KB | Display | |
Data in CIF | ![]() | 165.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yemC ![]() 7wcaC ![]() 4aumS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 79382.023 Da / Num. of mol.: 4 / Mutation: T188A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: M4GGR7, catalase #2: Chemical | ChemComp-HDD / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ALA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 42.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG400, Potassium chloride, Calcium chloride, Sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→112.6 Å / Num. obs: 520328 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.07 / Num. unique obs: 520328 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4AUM Resolution: 1.4→56.37 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.243 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.43 Å2 / Biso mean: 13.312 Å2 / Biso min: 4.34 Å2
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Refinement step | Cycle: final / Resolution: 1.4→56.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0
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