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- PDB-5cig: Complex of yeast cytochrome c peroxidase (W191G) with iso-1 cytoc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cig | ||||||||||||
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Title | Complex of yeast cytochrome c peroxidase (W191G) with iso-1 cytochrome c | ||||||||||||
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![]() | ELECTRON TRANSPORT-OXIDOREDUCTASE / electron transfer / heme proteins / electron hopping / multi-step tunneling / photochemistry / ELECTRON TRANSPORT-OXIDOREDUCTASE complex | ||||||||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / response to reactive oxygen species ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cytochrome-c peroxidase / 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 / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Crane, B.R. / Payne, T.M. | ||||||||||||
![]() | ![]() Title: Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c. Authors: Payne, T.M. / Yee, E.F. / Dzikovski, B. / Crane, B.R. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.8 KB | Display | ![]() |
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PDB format | ![]() | 146.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cibC ![]() 5cicC ![]() 5cidC ![]() 5cieC ![]() 5cifC ![]() 5cihC C: citing same article ( |
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Similar structure data |
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Links
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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: 33396.102 Da / Num. of mol.: 2 / Fragment: UNP residues 68-361 / Mutation: W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Plasmid: ppSUMO / Production host: ![]() ![]() #2: Protein | Mass: 12073.835 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Plasmid: PBTR-1 / Production host: ![]() ![]() #3: Chemical | ChemComp-HEC / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.98 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 15-15%, 100 mM NaAcetate, 175 mM NaCl / PH range: 4.8-5.6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 3, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→50 Å / Num. obs: 52508 / % possible obs: 96.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.121 / Χ2: 1.88 / Net I/av σ(I): 9.198 / Net I/σ(I): 12.6 / Num. measured all: 152557 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Resolution: 2.06→29.179 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.51 Å2 / Biso mean: 43.3453 Å2 / Biso min: 23.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.06→29.179 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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