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Yorodumi- PDB-6dky: Crystal structure of ribifolin, an orbitide from Jatropha ribifolia -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dky | |||||||||
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Title | Crystal structure of ribifolin, an orbitide from Jatropha ribifolia | |||||||||
Components | ILE-LEU-GLY-SER-ILE-ILE-LEU-GLY | |||||||||
Keywords | UNKNOWN FUNCTION / cyclic peptide | |||||||||
Biological species | Jatropha (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.239 Å | |||||||||
Authors | Wang, C.K. / Ramalho, S.D. / King, G.J. / Craik, D.J. | |||||||||
Funding support | Brazil, Australia, 2items
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Citation | Journal: J. Nat. Prod. / Year: 2018 Title: Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species. Authors: Ramalho, S.D. / Wang, C.K. / King, G.J. / Byriel, K.A. / Huang, Y.H. / Bolzani, V.S. / Craik, D.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dky.cif.gz | 9.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dky.ent.gz | 5.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/6dky ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dky | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 784.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Jatropha (plant) #2: 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: 1.72 Å3/Da / Density % sol: 28.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris base (pH 8.0) and 40% 2-methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.239→16.79 Å / Num. obs: 3333 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.239→1.284 Å / Rmerge(I) obs: 0.224 / Num. unique all: 292 |
-Processing
Software |
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Refinement | Resolution: 1.239→16.79 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.239→16.79 Å
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Refine LS restraints |
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LS refinement shell |
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