[English] 日本語
Yorodumi- PDB-5ebx: THE CRYSTAL STRUCTURE OF ERABUTOXIN A AT 2.0 ANGSTROMS RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ebx | ||||||
---|---|---|---|---|---|---|---|
Title | THE CRYSTAL STRUCTURE OF ERABUTOXIN A AT 2.0 ANGSTROMS RESOLUTION | ||||||
Components | ERABUTOXIN A | ||||||
Keywords | TOXIN | ||||||
Function / homology | Function and homology information acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Laticauda semifasciata (broad-banded blue sea krait) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Corfield, P.W.R. / Lee, T.-J. / Low, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1989 Title: The crystal structure of erabutoxin a at 2.0-A resolution. Authors: Corfield, P.W. / Lee, T.J. / Low, B.W. #1: Journal: Acta Crystallogr.,Sect.A / Year: 1988 Title: Refinement at 1.4 Angstroms Resolution of a Model of Erabutoxin B. Treatment of Ordered Solvent and Discrete Disorder Authors: Smith, J.L. / Corfield, P.W.R. / Hendrickson, W.A. / Low, B.W. #2: Journal: FEBS Lett. / Year: 1988 Title: Alpha-Toxin Binding to Acetylcholine Receptor Alpha 179-191 Peptides. Intrinsic Fluorescence Studies Authors: Radding, W. / Corfield, P.W.R. / Levinson, L.S. / Hashim, G.A. / Low, B.W. #3: Journal: Asia Pac.J.Pharmacol. / Year: 1987 Title: Acetylcholine Receptor. Alpha-Toxin Binding Site. Theoretical and Model Studies Authors: Low, B.W. / Corfield, P.W.R. #4: Journal: Eur.J.Biochem. / Year: 1985 Title: Erabutoxin B. Initial Protein Refinement and Sequence Analysis at 0.140 Nanometers Resolution Authors: Bourne, P.E. / Sato, A. / Corfield, P.W.R. / Rosen, L.S. / Birken, S. / Low, B.W. #5: Journal: Handb.Exp.Pharmacol. / Year: 1979 Title: The Three-Dimensional Structure of Postsynaptic Snake Neurotoxins. Consideration of Structure and Function Authors: Low, B.W. #6: Journal: J.Biol.Chem. / Year: 1971 Title: X-Ray Crystallographic Study of the Erabutoxins and of a Diiodo Derivative Authors: Low, B.W. / Potter, R. / Jackson, R.B. / Tamiya, N. / Sato, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ebx.cif.gz | 21.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ebx.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ebx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ebx_validation.pdf.gz | 372 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ebx_full_validation.pdf.gz | 372.2 KB | Display | |
Data in XML | 5ebx_validation.xml.gz | 3 KB | Display | |
Data in CIF | 5ebx_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/5ebx ftp://data.pdbj.org/pub/pdb/validation_reports/eb/5ebx | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 6853.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Laticauda semifasciata (broad-banded blue sea krait) References: UniProt: P60775 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Compound details | ERABUTOXINS A AND B ARE SHORT-CHAIN POSTSYNAPTIC NEUROTOXINS ISOLATED FROM THE VENOM OF THE SEA- ...ERABUTOXIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.39 % |
---|---|
Crystal grow | *PLUS Method: microdialysisDetails: referred to 'Tamiya.', (1966) Biochem.J., 99, 624-630 |
Components of the solutions | *PLUS Conc.: 0.85 % / Common name: sodium chloride |
-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 2714 / % possible obs: 75 % / Observed criterion σ(I): 2 / Num. measured all: 3640 |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→10 Å / σ(I): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 2680 / σ(I): 2 / Rfactor obs: 0.168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |