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- PDB-5t7h: Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5t7h | ||||||||||||
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Title | Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 | ||||||||||||
![]() | Cytochrome c iso-1 | ||||||||||||
![]() | ELECTRON TRANSPORT / cytochrome C / peroxidase activity / CYMAL6 | ||||||||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mcclelland, L. / Mou, T.C. / Sprang, S.R. / Bowler, B.E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons. Authors: McClelland, L.J. / Steele, H.B. / Whitby, F.G. / Mou, T.C. / Holley, D. / Ross, J.B. / Sprang, S.R. / Bowler, B.E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.3 KB | Display | ![]() |
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PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kkeC ![]() 5kluC ![]() 4mu8S S: Starting model for refinement 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: 12130.861 Da / Num. of mol.: 4 / Mutation: K72A, C10S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Plasmid: PRBS_BTR1 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ZE7 / #4: Chemical | ChemComp-HEC / #5: 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: 51.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 75% (NH4)2SO4, AN 86% (NH4)2SO4 AND 0.1 M TRIS RESERVOIR SOLUTION, AND 5.6 MM CYMAL-6., PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 21, 2015 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.003→27.15 Å / Num. obs: 31532 / % possible obs: 95.8 % / Redundancy: 1.7 % / Biso Wilson estimate: 30.42 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.003→2.08 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.26 / % possible all: 90.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MU8 Resolution: 2.003→7.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.003→7.98 Å
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Refine LS restraints |
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LS refinement shell |
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