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- PDB-1kxi: STRUCTURE OF CYTOTOXIN HOMOLOG PRECURSOR -

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Basic information

Entry
Database: PDB / ID: 1kxi
TitleSTRUCTURE OF CYTOTOXIN HOMOLOG PRECURSOR
ComponentsCARDIOTOXIN V
KeywordsCYTOTOXIN / VENOM / CARDIOTOXIN / MULTIGENE FAMILY
Function / homology
Function and homology information


other organism cell membrane / toxin activity / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / 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
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / Resolution: 2.19 Å
AuthorsSun, Y.-J. / Wu, W.-G. / Chiang, C.-M. / Hsin, A.-Y. / Hsiao, C.-D.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of cardiotoxin V from Taiwan cobra venom: pH-dependent conformational change and a novel membrane-binding motif identified in the three-finger loops of P-type cardiotoxin.
Authors: Sun, Y.J. / Wu, W.G. / Chiang, C.M. / Hsin, A.Y. / Hsiao, C.D.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Two Distinct Types of Cardiotoxin as Revealed by the Structure and Activity Relationship of Their Interaction with Zwitterionic Phospholipid Dispersions
Authors: Chien, K.Y. / Chiang, C.M. / Hseu, Y.C. / Vyas, A.A. / Rule, G.S. / Wu, W.G.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Fusion of Sphingomyelin Vesicles Induced by Proteins from Taiwan Cobra (Naja Naja Atra) Venom. Interactions of Zwitterionic Phospholipids with Cardiotoxin Analogues
Authors: Chien, K.Y. / Huang, W.N. / Jean, J.H. / Wu, W.G.
History
DepositionAug 29, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARDIOTOXIN V
B: CARDIOTOXIN V


Theoretical massNumber of molelcules
Total (without water)14,0552
Polymers14,0552
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.300, 43.300, 147.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CARDIOTOXIN V / CTX A5


Mass: 7027.456 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja atra (Chinese cobra) / Organ: VENOM GLAND / Production host: Escherichia coli (E. coli) / References: UniProt: P62375
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 18 K / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 %PEG40001drop
30.15 M1dropLi2SO4
40.1 MTris-HCl1drop
520 %PEG40001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 7280 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 2.19 Å / Num. measured all: 38418
Reflection shell
*PLUS
% possible obs: 82.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.19→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.305 -
Rwork0.207 -
obs0.207 7013
Displacement parametersBiso mean: 24.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.19→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 0 73 1047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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