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Yorodumi- PDB-3qyu: Crystal structure of human cyclophilin D at 1.54 A resolution at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qyu | ||||||
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Title | Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature | ||||||
Components | Peptidyl-prolyl cis-trans isomerase F | ||||||
Keywords | ISOMERASE / beta barrel / prolyl cis/trans isomerase / mitochondria | ||||||
Function / homology | Function and homology information regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / necroptotic process / apoptotic mitochondrial changes / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / isomorphous / Resolution: 1.54 Å | ||||||
Authors | Colliandre, L. / Gelin, M. / Labesse, G. / Guichou, J.-F. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: In-plate protein crystallization, in situ ligand soaking and X-ray diffraction. Authors: le Maire, A. / Gelin, M. / Pochet, S. / Hoh, F. / Pirocchi, M. / Guichou, J.F. / Ferrer, J.L. / Labesse, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qyu.cif.gz | 79 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qyu.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/3qyu ftp://data.pdbj.org/pub/pdb/validation_reports/qy/3qyu | HTTPS FTP |
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-Related structure data
Related structure data | 3qywC 3qyzC 2z6wS C: citing same article (ref.) 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: 17652.125 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIF, CYP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30405, peptidylprolyl isomerase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 30% Peg 4000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97964 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2010 | ||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 0.97964 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.54→28.976 Å / Num. all: 19640 / Num. obs: 18518 / % possible obs: 86.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % | ||||||||||||||||||
Reflection shell | Resolution: 1.54→1.62 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.2 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous Starting model: PDB entry 2Z6W Resolution: 1.54→27.53 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.184 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.086 / 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: 13.386 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→27.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.62 Å / Num. reflection Rwork: 1196 / Total num. of bins used: 20 |