3EBX

REFINEMENT AT 1.4 ANGSTROMS RESOLUTION OF A MODEL OF ERABUTOXIN B. TREATMENT OF ORDERED SOLVENT AND DISCRETE DISORDER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refinement at 1.4 A resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder.

Smith, J.L.Corfield, P.W.Hendrickson, W.A.Low, B.W.

(1988) Acta Crystallogr.,Sect.A 44: 357-368

  • DOI: 10.1107/s0108767388000303

  • PubMed Abstract: 
  • The latter stages in the refinement of the protein erabutoxin b are described. The crystal structure of the 62-residue protein has been refined to a conventional R factor of 0.144 by stereochemically restrained least-squares methods using diffraction ...

    The latter stages in the refinement of the protein erabutoxin b are described. The crystal structure of the 62-residue protein has been refined to a conventional R factor of 0.144 by stereochemically restrained least-squares methods using diffraction data to a limit of 1.4 A spacings. Emphasis was placed on determining as accurately as possible the solvent structure and the structures of heterogeneous groups in the protein. The final model includes two conformers for each of seven side chains and for an octapeptide segment. A total of 111 sites for water molecules have been located as well as one sulfate ion with a total of 68 site occupancies. 65 of the solvent sites overlap either with protein atoms belonging to groups in two alternative conformations or with other solvent sites. Dual protein conformers and overlapping solvent sites were both included in the least-squares refinement. Individual thermal and occupancy parameters were refined for solvent molecules. An analysis of these parameters has provided useful structural information.


    Related Citations: 
    • The Toxin-Agglutinin Fold. A New Group of Small Protein Structures Organized Around a Four-Disulfide Core
      Drenth, J.,Low, B.W.,Richardson, J.S.,Wright, C.S.
      (1980) J.Biol.Chem. 255: 2652
    • Three Dimensional Structure of Erabutoxin B Neurotoxic Protein. Inhibitor of Acetylcholine Receptor
      Low, B.W.,Preston, H.S.,Sato, A.,Rosen, L.S.,Searl, J.E.,Rudko, A.D.,Richardson, J.S.
      (1976) Proc.Natl.Acad.Sci.USA 73: 2991
    • Erabutoxin B. Structure(Slash)Function Relationships Following Initial Protein Refinement at 0.140-Nm Resolution
      Low, B.W.,Corfield, P.W.R.
      (1986) Eur.J.Biochem. 161: 579
    • Erabutoxin B. Initial Protein Refinement and Sequence Analysis at 0.140-Nm Resolution
      Bourne, P.E.,Sato, A.,Corfield, P.W.R.,Rosen, L.S.,Birken, S.,Low, B.W.
      (1985) Eur.J.Biochem. 153: 521
    • X-Ray Crystallographic Study of the Erabutoxins and of a Diiodo Derivative
      Low, B.W.,Potter, R.,Jackson, R.B.,Tamiya, N.,Sato, S.
      (1971) J.Biol.Chem. 246: 4366
    • Acetylcholine Receptor. Alpha-Toxin Binding Site-Theoretical and Model Studies
      Low, B.W.,Corfield, P.W.R.
      (1987) Asia Pac.J.Pharmacol. 2: 115
    • Molecular Conformation of Erabutoxin B. Atomic Coordinates at 2.5 Angstroms Resolution
      Kimball, M.R.,Sato, A.,Richardson, J.S.,Rosen, L.S.,Low, B.W.
      (1979) Biochem.Biophys.Res.Commun. 88: 950
    • The Three-Dimensional Structure of Postsynaptic Snake Neurotoxins. Consideration of Structure and Function
      Low, B.W.
      (1979) Handb.Exp.Pharmacol. 52: 213


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ERABUTOXIN B
A
62Laticauda semifasciataMutation(s): 0 
Find proteins for Q90VW1 (Laticauda semifasciata)
Go to UniProtKB:  Q90VW1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.940α = 90.00
b = 46.580β = 90.00
c = 21.590γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-04-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other