[English] 日本語
Yorodumi- PDB-6lsq: Crystal structure of Echistatin, an RGD-containing short disintegrin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lsq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Echistatin, an RGD-containing short disintegrin | ||||||
Components | Disintegrin | ||||||
Keywords | BLOOD CLOTTING / Disintegrin / Platelet aggregation inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Echis carinatus (saw-scaled viper) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chang, Y.T. / Chen, Y.C. / Chuang, W.J. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Toxins / Year: 2020 Title: Structural Insight into Integrin Recognition and Anticancer Activity of Echistatin. Authors: Chen, Y.C. / Chang, Y.T. / Chen, C.Y. / Shiu, J.H. / Cheng, C.H. / Huang, C.H. / Chen, J.F. / Chuang, W.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6lsq.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6lsq.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lsq ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lsq | HTTPS FTP |
---|
-Related structure data
Related structure data | 4rqgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 5711.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echis carinatus (saw-scaled viper) / Production host: Komagataella pastoris (fungus) / References: UniProt: E9JGG9 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.68 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Bicine pH9.0 2.55M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 7695 / % possible obs: 92.5 % / Redundancy: 4.9 % / CC1/2: 0.991 / Net I/σ(I): 7.88 |
Reflection shell | Resolution: 1.8→1.91 Å / Mean I/σ(I) obs: 2.96 / Num. unique obs: 2099 / CC1/2: 0.951 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RQG Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.493 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.851 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|