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- PDB-5kq6: Crystal structure of the A359D variant of catalase-peroxidase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kq6 | ||||||
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Title | Crystal structure of the A359D variant of catalase-peroxidase from B. pseudomallei | ||||||
![]() | Catalase-peroxidase | ||||||
![]() | OXIDOREDUCTASE / catalase / peroxidase / A359D / heme | ||||||
Function / homology | ![]() catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loewen, P.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Authors: Machuqueiro, M. / Victor, B. / Switala, J. / Villanueva, J. / Rovira, C. / Fita, I. / Loewen, 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 | ![]() | 581.8 KB | Display | ![]() |
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PDB format | ![]() | 470.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 72.1 KB | Display | |
Data in CIF | ![]() | 108.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kq0C ![]() 5kq2C ![]() 5kq3C ![]() 5kqhC ![]() 5kqiC ![]() 5kqkC ![]() 5ksfC ![]() 5kskC ![]() 5syuC ![]() 5syvC ![]() 5sywC ![]() 5txqC ![]() 5v4oC ![]() 5v53C ![]() 1mwv ![]() 5kq7 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 79612.992 Da / Num. of mol.: 2 / Mutation: A359D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1710b / Gene: katG, BURPS1710b_3366 / Plasmid: pKS / Production host: ![]() ![]() |
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-Non-polymers , 7 types, 1593 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MPD / ( #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.27 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MPD |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2015 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.62→96.52 Å / Num. all: 251711 / Num. obs: 251711 / % possible obs: 97.7 % / Redundancy: 4.7 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.049 / Rsym value: 0.044 / Net I/av σ(I): 13.307 / Net I/σ(I): 20.8 / Num. measured all: 1172517 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1MWV ![]() 1mwv Resolution: 1.62→47.8 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.842 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0628 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.066 / Details: MOLECULAR REPLACEMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.46 Å2 / Biso mean: 23.856 Å2 / Biso min: 9.98 Å2
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Refinement step | Cycle: final / Resolution: 1.62→47.8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.62→1.662 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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