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Yorodumi- PDB-1s6v: Structure of a cytochrome c peroxidase-cytochrome c site specific... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s6v | |||||||||
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Title | Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE / heme enzyme / electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX | |||||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cardiolipin binding / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | |||||||||
Authors | Guo, M. / Bhaskar, B. / Li, H. / Barrows, T.P. / Poulos, T.L. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Crystal structure and characterization of a cytochrome c peroxidase-cytochrome c site-specific cross-link Authors: Guo, M. / Bhaskar, B. / Li, H. / Barrows, T.P. / Poulos, T.L. #1: Journal: Science / Year: 1992 Title: Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c Authors: Pelletier, H. / Kraut, J. | |||||||||
History |
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Remark 999 | SEQUENCE The mutation of residue -5 (chains B and D) from Thr to Ala originated from cloning. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s6v.cif.gz | 188.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s6v.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 1s6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s6v_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1s6v_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1s6v_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 1s6v_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/1s6v ftp://data.pdbj.org/pub/pdb/validation_reports/s6/1s6v | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33543.188 Da / Num. of mol.: 2 / Mutation: C128A, V197C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1, CCP, CPO, YKR066C / Plasmid: pT7-7, pBTR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase #2: Protein | Mass: 12073.835 Da / Num. of mol.: 2 / Mutation: A81C, C102T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pT7-7, pBTR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00044 #3: Chemical | ChemComp-IOD / | #4: Chemical | ChemComp-HEC / #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: 46.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PEG 3350, KI, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. obs: 60567 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3 / Rsym value: 0.573 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→45.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1807586.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.7744 Å2 / ksol: 0.381001 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.88→45.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.95 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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