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- PDB-6ebx: STRUCTURE DETERMINATION OF A DIMERIC FORM OF ERABUTOXIN B, CRYSTA... -

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Basic information

Entry
Database: PDB / ID: 6ebx
TitleSTRUCTURE DETERMINATION OF A DIMERIC FORM OF ERABUTOXIN B, CRYSTALLIZED FROM THIOCYANATE SOLUTION
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 three-finger toxin / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Erabutoxin b
Similarity search - Component
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsPrange, T. / Saludjian, P.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure determination of a dimeric form of erabutoxin-b, crystallized from a thiocyanate solution.
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
#1: Journal: To be Published
Title: Crystallization of Basic Proteins by Ion Pairing
Authors: Ries-Kautt, M. / Ducruix, A.
#2: Journal: J.Biol.Chem. / Year: 1988
Title: Relative Effectiveness of Various Ions on the Solubility and Crystal Growth of Lysozyme
Authors: Ries-Kautt, M. / Ducruix, A.
#3: Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: Refinement at 1.4 Angstrom Resolution of a Model of Erabutoxin B: Treatment of Ordered Solvent and Discrete Disorder
Authors: Smith, J.L. / Hendrickson, P.W.R.Corfield.W.A. / Low, B.W.
#4: 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.
#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.
History
DepositionMay 31, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: 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 23, 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE TWO MOLECULES ARE ASSOCIATED VIA 1) AN INTERMOLECULAR ANTI-PARALLEL BETA SHEET ...SHEET THE TWO MOLECULES ARE ASSOCIATED VIA 1) AN INTERMOLECULAR ANTI-PARALLEL BETA SHEET ASSOCIATION AROUND THE TWO-FOLD NON-CRYSTALLOGRAPHIC AXIS AND 2) VIA INTERLEAVING OF FINGERS TWO AND THREE WITH MUTUAL TRP-29/PHE-32 STACKING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ERABUTOXIN B
B: ERABUTOXIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8143
Polymers13,7562
Non-polymers581
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.360, 40.890, 55.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ERABUTOXIN B


Mass: 6877.759 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Laticauda semifasciata (broad-banded blue sea krait)
References: UniProt: Q90VW1
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growDetails: CRYSTALLIZATION TOOK PLACE FROM KSCN SOLUTION (O.3M) AT PH 5.5 BY THE HANGING DROP METHOD AT ROOM TEMPERATURE. CRYSTALS APPEARED IN TWO WEEKS AS ELONGATED RODS.
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mMprotein1drop
20.15 MKSCN1drop
350 mMacetate1drop
40.3 MKSCN1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 11227 / % possible obs: 82 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.82 Å / Num. possible: 64 / Num. unique obs: 1577

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 1.7 Å
Details: SHIFTS FROM ENTRY *2EBX* IN POSITIONS OF NON-DISORDERED PROTEIN ATOMS ARE SMALL. THE RMS DEVIATION IS 0.5 ANGSTROMS FOR MAIN CHAIN ATOMS AND 0.9 FOR THE SIDE CHAIN ATOMS.
RfactorNum. reflection
Rwork0.194 -
obs-10913
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 3 97 1056
Software
*PLUS
Name: 'X-PLOR, PROLSQ' / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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