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- PDB-1qkd: ERABUTOXIN -

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Basic information

Entry
Database: PDB / ID: 1qkd
TitleERABUTOXIN
ComponentsERABUTOXIN A
KeywordsNEUROTOXIN / ERABUTOXIN
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsNastopoulos, V. / Kanellopoulos, P.N. / Tsernoglou, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of dimeric and monomeric erabutoxin a refined at 1.5 A resolution.
Authors: Nastopoulos, V. / Kanellopoulos, P.N. / Tsernoglou, D.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERABUTOXIN A
B: ERABUTOXIN A


Theoretical massNumber of molelcules
Total (without water)13,7072
Polymers13,7072
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.320, 53.540, 40.760
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: (-0.998, -0.0264, -0.0579), (-0.0635, 0.3626, 0.9298), (-0.0035, 0.9316, -0.3635)
Vector: 48.3697, -8.311, 14.5737)

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Components

#1: Protein ERABUTOXIN A


Mass: 6853.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: JAPANESE SEA SNAKE
Source: (natural) Laticauda semifasciata (broad-banded blue sea krait)
Secretion: VENOM / References: UniProt: P60775
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 44.1 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
240 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.49→17.4 Å / Num. obs: 19420 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.065 / Net I/σ(I): 29.7
Reflection shellResolution: 1.49→1.6 Å / Redundancy: 14 % / Mean I/σ(I) obs: 5.25 / Rsym value: 0.204 / % possible all: 86
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 86 % / Rmerge(I) obs: 0.204

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EBX

6ebx


Resolution: 1.49→17.4 Å / σ(F): 0 / Details: X-PLOR WAS ALSO USED
RfactorNum. reflection% reflection
all0.169 --
obs-19420 100 %
Refinement stepCycle: LAST / Resolution: 1.49→17.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 206 1193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.17
X-RAY DIFFRACTIONt_dihedral_angle_d18.13
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005
X-RAY DIFFRACTIONt_gen_planes0.013
X-RAY DIFFRACTIONt_it7.22
X-RAY DIFFRACTIONt_nbd0.04
Software
*PLUS
Name: TNT / Version: 5EA / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.13
X-RAY DIFFRACTIONt_plane_restr0.013

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