+Open data
-Basic information
Entry | Database: PDB / ID: 6c4w | ||||||
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Title | Structure of the yeast Pichia membranifaciens cytochrome c | ||||||
Components | cytochrome c | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT (CYTOCHROME) HEMEC / yeast / Saccharomyces / Molecular replacement / Valida | ||||||
Function / homology | Function and homology information respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pichia membranifaciens (yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | McPherson, A. | ||||||
Citation | Journal: to be published Title: Characterization of two crystal forms of cytochrome c from Valida membranifaciens Authors: Day, J. / McPherson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c4w.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c4w.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 6c4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/6c4w ftp://data.pdbj.org/pub/pdb/validation_reports/c4/6c4w | HTTPS FTP |
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-Related structure data
Related structure data | 1yccS 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: 12181.007 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pichia membranifaciens (yeast) / References: UniProt: A0A3B6UES8*PLUS |
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#2: Chemical | ChemComp-HEC / |
#3: 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: 2.4 Å3/Da / Density % sol: 49 % / Description: thin rectangular laths |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.25 / Details: 25% PEG 4000, 0.1 M Tris-HCl, pH 8.25 / PH range: 8.0 8.5 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Dec 25, 1990 |
Radiation | Monochromator: Supper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 4586 / % possible obs: 95.8 % / Redundancy: 2.2 % / CC1/2: 0.951 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.133 / Rrim(I) all: 0.223 / Rsym value: 0.161 / Net I/av σ(I): 3.2 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 436 / CC1/2: 0.747 / Rpim(I) all: 0.273 / Rrim(I) all: 0.446 / Rsym value: 0.347 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ycc Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.812 / SU B: 32.905 / SU ML: 0.374 / Cross valid method: FREE R-VALUE / ESU R: 0.779 / ESU R Free: 0.389 / 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: 38.586 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→15 Å
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Refine LS restraints |
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