+Open data
-Basic information
Entry | Database: PDB / ID: 1rz6 | |||||||||
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Title | Di-haem Cytochrome c Peroxidase, Form IN | |||||||||
Components | Cytochrome c peroxidase | |||||||||
Keywords | OXIDOREDUCTASE / PEROXIDASE / HAEM / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Marinobacter hydrocarbonoclasticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Dias, J.M. / Alves, T. / Bonifacio, C. / Pereira, A. / Bourgeois, D. / Moura, I. / Romao, M.J. | |||||||||
Citation | Journal: Structure / Year: 2004 Title: Structural basis for the mechanism of Ca(2+) activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617. Authors: Dias, J.M. / Alves, T. / Bonifacio, C. / Pereira, A.S. / Trincao, J. / Bourgeois, D. / Moura, I. / Romao, M.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and preliminary X-ray diffraction analysis of two pH-dependent forms of a di-haem cytochrome c peroxidase from Pseudomonas nautica Authors: Dias, J.M. / Bonifacio, C. / Alves, T. / Moura, J.J. / Moura, I. / Romao, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rz6.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rz6.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rz6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1rz6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1rz6_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1rz6_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rz6 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rz6 | HTTPS FTP |
-Related structure data
Related structure data | 1nmlC 1rz5SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35383.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Marinobacter hydrocarbonoclasticus (bacteria) Strain: 617 / References: UniProt: P83787, cytochrome-c peroxidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-CIT / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 70.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. all: 40388 / Num. obs: 40388 / % possible obs: 99.9 % / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1RZ5 Resolution: 2.2→25 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→25 Å
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Refine LS restraints |
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