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- PDB-3era: RECOMBINANT ERABUTOXIN A (S8T MUTANT) -

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Basic information

Entry
Database: PDB / ID: 3era
TitleRECOMBINANT ERABUTOXIN A (S8T MUTANT)
ComponentsERABUTOXIN A
KeywordsNEUROTOXIN / SNAKE NEUROTOXIN / VENOM / POSTSYNAPTIC NEUROTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Erabutoxin a
Similarity search - Component
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR / Resolution: 1.7 Å
AuthorsGaucher, J.F. / Menez, R. / Arnoux, B. / Menez, A. / Ducruix, A.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: High resolution x-ray analysis of two mutants of a curaremimetic snake toxin
Authors: Gaucher, J.F. / Menez, R. / Arnoux, B. / Menez, A. / Ducruix, A.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Genetic Engineering of Snake Toxins. The Functional Site of Erabutoxin A, as Delineated by Site-Directed Mutagenesis, Includes Variant Residues
Authors: Tremeau, O. / Lemaire, C. / Drevet, P. / Pinkasfeld, S. / Ducancel, F. / Boulain, J.C. / Menez, A.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Genetic Engineering of Snake Toxins. Role of Invariant Residues in the Structural and Functional Properties of a Curaremimetic Toxin, as Probed by Site-Directed Mutagenesis
Authors: Pillet, L. / Tremeau, O. / Ducancel, F. / Drevet, P. / Zinn-Justin, S. / Pinkasfeld, S. / Boulain, J.C. / Menez, A.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of a Dimeric Form of Erabutoxin-B, Crystallized from Thiocyanate Solution
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
#4: 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.
#5: 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.R. / Hendrickson, W.A. / Low, B.W.
History
DepositionJun 25, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,9105
Polymers13,7352
Non-polymers1743
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.418, 53.013, 40.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99975, -0.00367, 0.02204), (0.01952, 0.33621, 0.94158), (-0.01087, 0.94178, -0.33606)
Vector: 47.12906, 25.64156, -36.72058)

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Components

#1: Protein ERABUTOXIN A


Mass: 6867.741 Da / Num. of mol.: 2 / Mutation: S8T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Laticauda semifasciata (broad-banded blue sea krait)
Plasmid: PEZZ 18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB 101 / References: UniProt: P60775
#2: Chemical ChemComp-SCN / THIOCYANATE ION


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


Mass: 18.015 Da / Num. of mol.: 116 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: CRYSTALLIZATION WERE PERFORMED AT 291K BY THE HANGING DROP METHOD. DROPS OF 2 MICROLITRE OF 0.007M PROTEIN AND 2 MICROLITRE OF RESERVOIR WERE EQUILIBRATED AGAINST 0.32M NASCN, 0.05M NAOAC ...Details: CRYSTALLIZATION WERE PERFORMED AT 291K BY THE HANGING DROP METHOD. DROPS OF 2 MICROLITRE OF 0.007M PROTEIN AND 2 MICROLITRE OF RESERVOIR WERE EQUILIBRATED AGAINST 0.32M NASCN, 0.05M NAOAC BUFFER SOLUTION (PH 4.5), vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mMtoxin1drop
2210 mM1reservoirNaSCN
350 mM1reservoirNaOAc

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.7→13.9 Å / Num. obs: 13459 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.29 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 13852 / % possible obs: 97.8 % / Num. measured all: 46741 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAAGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR
Starting model: STRUCTURE OF RECOMBINANT ERABUTOXIN A (S8G MUTANT)

Resolution: 1.7→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: AT THE END OF REFINEMENT RFREE DATA SET WAS COMBINED WITH OTHER DATA FOR THE LAST STEP OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1243 9.9 %RANDOM
Rwork0.179 ---
obs0.179 12566 96.9 %-
Displacement parametersBiso mean: 15.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.18 Å
Luzzati d res low-10 Å
Luzzati sigma a-0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 9 116 1083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.95
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.251 125 9.1 %
Rwork0.24 1248 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.24

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