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Yorodumi- PDB-5ncv: Crystal Structure of Cytochrome c in complex with p-Methylphospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ncv | ||||||
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Title | Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene | ||||||
Components | Cytochrome c iso-1 | ||||||
Keywords | OXIDOREDUCTASE / methylphosphonatocalix[4]arene / cytochrome c / lysine recognition / protein assembly | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / 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: 1.5 Å | ||||||
Authors | Alex, J.M. / Rennie, M.L. / Crowley, P.B. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Cryst.Growth Des. / Year: 2018 Title: Phosphonated Calixarene as a ""Molecular Glue"" for Protein Crystallization Authors: Alex, J.M. / Rennie, M.L. / Volpi, S. / Sansone, F. / Casnati, A. / Crowley, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ncv.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ncv.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ncv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ncv_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5ncv_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 5ncv_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5ncv_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/5ncv ftp://data.pdbj.org/pub/pdb/validation_reports/nc/5ncv | HTTPS FTP |
-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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12041.770 Da / Num. of mol.: 2 / Mutation: T-5A, C102T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CYC1, YJR048W, J1653 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00044 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20 % PEG 8000, 50 mM NaCl, 50 mM sodium acetate (pH 5.6). [Cytochrome c] = 0.75 mM and [Methylphosphonatocalix[4]arene] = 0.3 mM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.74 Å / Num. obs: 34591 / % possible obs: 99.2 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.026 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.055 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3452 / Rpim(I) all: 0.158 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YCC Resolution: 1.5→47.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.649 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.081 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 143.7 Å2 / Biso mean: 20.624 Å2 / Biso min: 9.15 Å2
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Refinement step | Cycle: final / Resolution: 1.5→47.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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