+Open data
-Basic information
Entry | Database: PDB / ID: 5jhx | ||||||
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Title | Crystal Structure of Fungal MagKatG2 at pH 3.0 | ||||||
Components | Catalase-peroxidase 2 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Magnaporthe oryzae (rice blast fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Gasselhuber, B. / Obinger, C. / Carpena, X. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase. Authors: Gasselhuber, B. / Graf, M.M. / Jakopitsch, C. / Zamocky, M. / Nicolussi, A. / Furtmuller, P.G. / Oostenbrink, C. / Carpena, X. / Obinger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jhx.cif.gz | 613.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jhx.ent.gz | 496.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/5jhx ftp://data.pdbj.org/pub/pdb/validation_reports/jh/5jhx | HTTPS FTP |
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-Related structure data
Related structure data | 5jhyC 5jhzC 3ut2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 83460.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus) Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: KATG2, CPXB, MagKatG2, MGG_09834 / Production host: Escherichia coli (E. coli) / References: UniProt: A4QUT2, catalase-peroxidase #2: Chemical | #3: Chemical | ChemComp-FLC / #4: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 15% PEG4000, 0.1 M sodium acetate, pH 4.6 (+ pH 3 sodium citrate soaking) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9729 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9729 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 293409 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.064 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.4 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UT2 Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.49 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.05 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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