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- PDB-3ebx: REFINEMENT AT 1.4 ANGSTROMS RESOLUTION OF A MODEL OF ERABUTOXIN B... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ebx | |||||||||
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Title | REFINEMENT AT 1.4 ANGSTROMS RESOLUTION OF A MODEL OF ERABUTOXIN B. TREATMENT OF ORDERED SOLVENT AND DISCRETE DISORDER | |||||||||
![]() | ERABUTOXIN B | |||||||||
![]() | TOXIN | |||||||||
Function / homology | ![]() acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Smith, J.L. / Corfield, P.W.R. / Hendrickson, W.A. / Low, B.W. | |||||||||
![]() | ![]() Title: Refinement at 1.4 A resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder. Authors: Smith, J.L. / Corfield, P.W. / Hendrickson, W.A. / Low, B.W. #1: ![]() Title: Acetylcholine Receptor. Alpha-Toxin Binding Site-Theoretical and Model Studies Authors: Low, B.W. / Corfield, P.W.R. #2: ![]() Title: Erabutoxin B. Structure(Slash)Function Relationships Following Initial Protein Refinement at 0.140-Nm Resolution Authors: Low, B.W. / Corfield, P.W.R. #3: ![]() Title: Erabutoxin B. Initial Protein Refinement and Sequence Analysis at 0.140-Nm Resolution Authors: Bourne, P.E. / Sato, A. / Corfield, P.W.R. / Rosen, L.S. / Birken, S. / Low, B.W. #4: ![]() Title: The Toxin-Agglutinin Fold. A New Group of Small Protein Structures Organized Around a Four-Disulfide Core Authors: Drenth, J. / Low, B.W. / Richardson, J.S. / Wright, C.S. #5: ![]() Title: Molecular Conformation of Erabutoxin B. Atomic Coordinates at 2.5 Angstroms Resolution Authors: Kimball, M.R. / Sato, A. / Richardson, J.S. / Rosen, L.S. / Low, B.W. #6: ![]() Title: The Three-Dimensional Structure of Postsynaptic Snake Neurotoxins. Consideration of Structure and Function Authors: Low, B.W. #7: ![]() Title: Three Dimensional Structure of Erabutoxin B Neurotoxic Protein. Inhibitor of Acetylcholine Receptor Authors: Low, B.W. / Preston, H.S. / Sato, A. / Rosen, L.S. / Searl, J.E. / Rudko, A.D. / Richardson, J.S. #8: ![]() 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 |
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Remark 700 | SHEET THE BETA SHEET *DCE* WAS INADVERTENTLY NOT INCLUDED IN ENTRY *2EBX*. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 25.9 KB | Display | ![]() |
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PDB format | ![]() | 19.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 404.8 KB | Display | ![]() |
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Full document | ![]() | 406.3 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 4. |
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Components
#1: Protein | Mass: 6877.759 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() References: UniProt: Q90VW1 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | THE POSTSYNAPTIC NEUROTOXINS OF SEA SNAKE VENOM ARE ANTAGONISTS OF THE NICOTINIC ACETYLCHOLINE ...THE POSTSYNAPT |
Source details | THE PREVIOUS REFINEMENT ESTABLISHED THE STRUCTURAL IDENTITY OF ERABUTOXIN B AND NEUROTOXIN B. ...THE PREVIOUS REFINEMENT |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.58 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: unknown / Details: referred to FEBS Lett.68.1-4 1976 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.4→10 Å / σ(F): 2 Details: SHIFTS FROM ENTRY *2EBX* IN POSITIONS OF NON-DISORDERED PROTEIN ATOMS ARE VERY SMALL. THE RMS DEVIATION IS 0.5 ANGSTROMS FOR ALL NON-DISORDERED ATOMS AND 0.07 ANGSTROMS FOR MAIN CHAIN ATOMS.
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / Num. reflection obs: 7732 / σ(F): 2 / Rfactor obs: 0.14 | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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