+Open data
-Basic information
Entry | Database: PDB / ID: 4q5p | ||||||
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Title | Lysine-Ligated Yeast Iso-1 Cytochrome C | ||||||
Components | Cytochrome c iso-1 | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information 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 / : / 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 / : / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Amacher, J.F. / Zhu, M.Q. / Zhong, F. / Pletneva, E.V. / Madden, D.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch. Authors: Amacher, J.F. / Zhong, F. / Lisi, G.P. / Zhu, M.Q. / Alden, S.L. / Hoke, K.R. / Madden, D.R. / Pletneva, E.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q5p.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q5p.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q5p_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4q5p_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4q5p_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 4q5p_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/4q5p ftp://data.pdbj.org/pub/pdb/validation_reports/q5/4q5p | HTTPS FTP |
-Related structure data
Related structure data | 1yeaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 11699.359 Da / Num. of mol.: 3 / Fragment: UNP residues 7-109 / Mutation: T78C, K79G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli (E. coli) / References: UniProt: P00044 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2 M ammonium phosphate, pH 8.1, 30% w/v PEG300, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2013 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.87→19.52 Å / Num. all: 35597 / Num. obs: 35544 / % possible obs: 99.9 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 29.96 / Rmerge(I) obs: 0.072 / Rsym value: 0.07 / Net I/σ(I): 29.96 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YEA Resolution: 1.87→19.52 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.213 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→19.52 Å
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Refine LS restraints |
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