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- PDB-3ebx: REFINEMENT AT 1.4 ANGSTROMS RESOLUTION OF A MODEL OF ERABUTOXIN B... -

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Basic information

Entry
Database: PDB / ID: 3ebx
TitleREFINEMENT AT 1.4 ANGSTROMS RESOLUTION OF A MODEL OF ERABUTOXIN B. TREATMENT OF ORDERED SOLVENT AND DISCRETE DISORDER
ComponentsERABUTOXIN B
KeywordsTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsSmith, J.L. / Corfield, P.W.R. / Hendrickson, W.A. / Low, B.W.
Citation
Journal: Acta Crystallogr.,Sect.A / Year: 1988
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: 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.
#2: Journal: Eur.J.Biochem. / Year: 1986
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: Journal: Eur.J.Biochem. / Year: 1985
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: Journal: J.Biol.Chem. / Year: 1980
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: Journal: Biochem.Biophys.Res.Commun. / Year: 1979
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: Journal: Handb.Exp.Pharmacol. / Year: 1979
Title: The Three-Dimensional Structure of Postsynaptic Snake Neurotoxins. Consideration of Structure and Function
Authors: Low, B.W.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1976
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: 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
DepositionJan 15, 1988Processing site: BNL
SupersessionApr 16, 1988ID: 2EBX
Revision 1.0Apr 16, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE BETA SHEET *DCE* WAS INADVERTENTLY NOT INCLUDED IN ENTRY *2EBX*.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERABUTOXIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9742
Polymers6,8781
Non-polymers961
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.940, 46.580, 21.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 4.

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Components

#1: Protein ERABUTOXIN B


Mass: 6877.759 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: Q90VW1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE POSTSYNAPTIC NEUROTOXINS OF SEA SNAKE VENOM ARE ANTAGONISTS OF THE NICOTINIC ACETYLCHOLINE ...THE POSTSYNAPTIC NEUROTOXINS OF SEA SNAKE VENOM ARE ANTAGONISTS OF THE NICOTINIC ACETYLCHOLINE RECEPTOR. THE HOMOLOGY BETWEEN ALL THESE VENOM NEUROTOXINS OF BOTH SHORT AND LONG CHAIN SERIES IS ACKNOWLEDGED IN SOME PUBLICATIONS BY SEQUENCE NUMBER CHANGES (SEE REFERENCE 6 ABOVE FOR DETAILS).
Source detailsTHE PREVIOUS REFINEMENT ESTABLISHED THE STRUCTURAL IDENTITY OF ERABUTOXIN B AND NEUROTOXIN B. ...THE PREVIOUS REFINEMENT ESTABLISHED THE STRUCTURAL IDENTITY OF ERABUTOXIN B AND NEUROTOXIN B. ERABUTOXIN B WAS ISOLATED FROM THE VENOM OF LATICAUDA SEMIFASCIATA FOUND OFF THE OKINAWAS (RYUKU ISLANDS). NEUROTOXIN B WAS ALSO ISOLATED FROM THE VENOM OF LATICAUDA SEMIFASCIATA BUT FOUND IN DIFFERENT PACIFIC OCEAN WATERS. PREVIOUS CHEMICAL SEQUENCE ERRORS IN THESE TOXINS AT HIS 6-GLU 7 AND SER 18-PRO 19 WERE CORRECTED IN ENTRY *2EBX*. THE CHEMICAL DESIGNATION VAL 59 (CITED AS ARG 59 IN NEUROTOXIN B) WAS ALSO UNAMBIGUOUSLY VERIFED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown / Details: referred to FEBS Lett.68.1-4 1976
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %satammonium sulfate12
25 mMphosphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 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.
RfactorNum. reflection
all0.176 10405
obs0.14 7732
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 0 5 111 685
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_deg1.5
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
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg0.030.033
X-RAY DIFFRACTIONp_planar_d0.060.049
X-RAY DIFFRACTIONp_plane_restr0.020.016
X-RAY DIFFRACTIONp_chiral_restr0.150.175
X-RAY DIFFRACTIONp_mcbond_it1.51.23
X-RAY DIFFRACTIONp_scbond_it22.49
X-RAY DIFFRACTIONp_mcangle_it21.84
X-RAY DIFFRACTIONp_scangle_it33.67

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