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Yorodumi- PDB-4hy7: Structural and biochemical characterization of a cytosolic wheat ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hy7 | ||||||
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Title | Structural and biochemical characterization of a cytosolic wheat cyclophilin TaCypA-1 | ||||||
Components |
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Keywords | ISOMERASE/INHIBITOR / ISOMERASE / ISOMERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm Similarity search - Function | ||||||
Biological species | Triticum aestivum (bread wheat) Tolypocladium inflatum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Sekhon, S.S. / Jeong, D.G. / Woo, E.J. / Singh, P. / Pareek, A. / Yoon, T.-S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural and biochemical characterization of the cytosolic wheat cyclophilin TaCypA-1. Authors: Sekhon, S.S. / Kaur, H. / Dutta, T. / Singh, K. / Kumari, S. / Kang, S. / Park, S.G. / Park, B.C. / Jeong, D.G. / Pareek, A. / Woo, E.J. / Singh, P. / Yoon, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hy7.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hy7.ent.gz | 36.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/4hy7 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/4hy7 | HTTPS FTP |
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-Related structure data
Related structure data | 4e1qSC S: Starting model for refinement C: citing same article (ref.) |
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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: 18416.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: CyP3, CyP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93W25, peptidylprolyl isomerase |
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#2: Protein/peptide | Type: Cyclic peptide / Class: ImmunosuppressantImmunosuppressive drug / Mass: 1220.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CYCLOSPORIN IS A CYCLIC UNDECAPEPTIDE. CYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI. Source: (natural) Tolypocladium inflatum (fungus) / References: NOR: NOR00033, Cyclosporin A |
#3: Water | ChemComp-HOH / |
Compound details | CYCLOSPORI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 197 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Wavelength: 0.9733 Å | ||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2012 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 0.9733 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. all: 47120 / Num. obs: 47120 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 | ||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E1Q Resolution: 1.2→27.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 0.565 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 11.143 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→27.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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