+Open data
-Basic information
Entry | Database: PDB / ID: 3hq8 | ||||||
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Title | CcpA from G. sulfurreducens S134P/V135K variant | ||||||
Components | Cytochrome c551 peroxidase | ||||||
Keywords | OXIDOREDUCTASE / cytochrome c peroxidase / Peroxidase | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase activity / electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacter sulfurreducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hoffmann, M. / Seidel, J. / Einsle, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: CcpA from Geobacter sulfurreducens is a basic di-heme cytochrome c peroxidase. Authors: Hoffmann, M. / Seidel, J. / Einsle, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hq8.cif.gz | 139.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hq8.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/3hq8 ftp://data.pdbj.org/pub/pdb/validation_reports/hq/3hq8 | HTTPS FTP |
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-Related structure data
Related structure data | 3hq6SC 3hq7C 3hq9C 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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-Components
#1: Protein | Mass: 36971.316 Da / Num. of mol.: 2 / Mutation: S134P,V135K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: ccpA, ccpA-2, GSU2813 / Production host: Escherichia coli (E. coli) / References: UniProt: Q749D0, cytochrome-c peroxidase #2: Chemical | ChemComp-HEM / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.05 Å |
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Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→70 Å / Num. obs: 27650 / % possible obs: 98.7 % / Redundancy: 3.4 % / Rsym value: 0.17 / Net I/σ(I): 6.3 |
-Processing
Software | Name: REFMAC / Version: 5.5.0072 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HQ6 Resolution: 2.4→44.77 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.861 / SU B: 16.138 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.351 / 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: 41.703 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→44.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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