[English] 日本語
Yorodumi- PDB-6dkz: Racemic structure of ribifolin, an orbitide from Jatropha ribifolia -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dkz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Racemic structure of ribifolin, an orbitide from Jatropha ribifolia | |||||||||
Components | ribifolin | |||||||||
Keywords | PLANT PROTEIN / cyclic peptide | |||||||||
Biological species | Jatropha ribifolia (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.99 Å | |||||||||
Authors | Wang, C.K. / King, G.J. / Ramalho, S.D. | |||||||||
Funding support | Brazil, Australia, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dkz.cif.gz | 11.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dkz.ent.gz | 7 KB | Display | PDB format |
PDBx/mmJSON format | 6dkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dkz_validation.pdf.gz | 337.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dkz_full_validation.pdf.gz | 337.5 KB | Display | |
Data in XML | 6dkz_validation.xml.gz | 1.3 KB | Display | |
Data in CIF | 6dkz_validation.cif.gz | 1.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/6dkz ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dkz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 784.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Jatropha ribifolia (plant) |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.86 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: in 0.1 M Tris base (pH 8.0) and 40% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 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: 0.99→19.86 Å / Num. obs: 5474 / % possible obs: 94.4 % / Redundancy: 6.5 % / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 0.99→1.01 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 0.99→11.473 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 13.1 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→11.473 Å /
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|