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Yorodumi- PDB-6k9i: High-resolution three-dimensional structure of horse heart cytoch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k9i | ||||||
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Title | High-resolution three-dimensional structure of horse heart cytochrome C at room temperature | ||||||
Components | Cytochrome c | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process ...cytochrome c-heme linkage / cytochrome complex / positive regulation of cysteine-type endopeptidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / mitochondrial intermembrane space / electron transfer activity / positive regulation of apoptotic process / lipid binding / apoptotic process / heme binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sugawara, Y. / Endo, S. | ||||||
Citation | Journal: To Be Published Title: High-resolution three-dimensional structure of horse heart cytochrome C Authors: Fujita, T. / Yamamura, S. / Endo, S. / Sugawara, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k9i.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k9i.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 6k9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k9i_validation.pdf.gz | 815.9 KB | Display | wwPDB validaton report |
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Full document | 6k9i_full_validation.pdf.gz | 816.4 KB | Display | |
Data in XML | 6k9i_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 6k9i_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/6k9i ftp://data.pdbj.org/pub/pdb/validation_reports/k9/6k9i | HTTPS FTP |
-Related structure data
Related structure data | 1hrcS 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
#1: Protein | Mass: 11751.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00004 |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 1.0-1.5M sodium chloride, 2.7-3.2M ammonium sulfate, 0.1M sodium phosphate Temp details: ROOM TEMERATURE |
-Data collection
Diffraction | Mean temperature: 293 K / Ambient temp details: ROOM TEMERATURE / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→23.9569 Å / Num. obs: 13227 / % possible obs: 99.9 % / Redundancy: 3.48 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 1292 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HRC Resolution: 1.8→19.72 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.784 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.098 / 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: 36.311 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→19.72 Å
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Refine LS restraints |
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