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Yorodumi- PDB-6ff5: X-ray structure of bovine heart cytochrome c at high ionic strength -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ff5 | ||||||
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Title | X-ray structure of bovine heart cytochrome c at high ionic strength | ||||||
Components | Cytochrome c | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome c | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity / heme binding / apoptotic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: Biometals / Year: 2018 Title: X-ray structure of bovine heart cytochrome c at high ionic strength. Authors: Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ff5.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ff5.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ff5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ff5_validation.pdf.gz | 838.4 KB | Display | wwPDB validaton report |
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Full document | 6ff5_full_validation.pdf.gz | 839.8 KB | Display | |
Data in XML | 6ff5_validation.xml.gz | 8 KB | Display | |
Data in CIF | 6ff5_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/6ff5 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/6ff5 | HTTPS FTP |
-Related structure data
Related structure data | 2b4zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11595.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62894 | ||||
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#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | ChemComp-NO3 / #4: Chemical | ChemComp-SO4 / | #5: 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: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.2-3.4 M ammonium sulfate and 0.4-0.5 M NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→56.9 Å / Num. obs: 12830 / % possible obs: 99.6 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.74→1.78 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 3810 / CC1/2: 0.725 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B4Z Resolution: 1.74→56.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.318 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.657 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→56.9 Å
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Refine LS restraints |
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