+Open data
-Basic information
Entry | Database: PDB / ID: 5xy4 | ||||||
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Title | CATPO mutant - V536W | ||||||
Components | Catalase | ||||||
Keywords | OXIDOREDUCTASE / catalase / phenol oxidase / lateral channel / mutant | ||||||
Function / homology | Function and homology information catalase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycothermus thermophilus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yuzugullu Karakus, Y. / Goc, G. / Balci, S. / Pearson, A.R. / Yorke, B. | ||||||
Funding support | Turkey, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Identification of the site of oxidase substrate binding in Scytalidium thermophilum catalase. Authors: Yuzugullu Karakus, Y. / Goc, G. / Balci, S. / Yorke, B.A. / Trinh, C.H. / McPherson, M.J. / Pearson, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xy4.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5xy4.ent.gz | 898 KB | Display | PDB format |
PDBx/mmJSON format | 5xy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xy4 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xy4 | HTTPS FTP |
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-Related structure data
Related structure data | 5xvzC 5y17C 5zz1C 4aumS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 21 - 698 / Label seq-ID: 1 - 678
NCS ensembles :
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-Components
#1: Protein | Mass: 74843.109 Da / Num. of mol.: 4 / Fragment: UNP residues 22-699 / Mutation: V536W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycothermus thermophilus (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: M4GGR7, catalase #2: Chemical | ChemComp-HDD / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-P6G / | #5: 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: 2.29 Å3/Da / Density % sol: 46.33 % |
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Crystal grow | Temperature: 323 K / Method: vapor diffusion, hanging drop Details: PEG400, Potassium chloride, Calcium chloride, Sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100.37 Å / Num. obs: 252686 / % possible obs: 90 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.047 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11150 / CC1/2: 0.643 / Rpim(I) all: 0.455 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AUM Resolution: 1.8→90.46 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.052 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.122 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.712 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→90.46 Å
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Refine LS restraints |
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