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- PDB-1ug4: Crystal Structure of Cardiotoxin VI from Taiwan Cobra (Naja atra)... -

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Basic information

Entry
Database: PDB / ID: 1ug4
TitleCrystal Structure of Cardiotoxin VI from Taiwan Cobra (Naja atra) Venom
ComponentsCytotoxin 6
KeywordsTOXIN / cardiotoxin / cobra / venom
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region
Similarity search - Function
Snake cytotoxin, cobra-type / 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 speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChung, F.-Y. / Wu, W.-G. / Chen, C.-J.
CitationJournal: Biochemistry / Year: 2005
Title: Structural difference between group I and group II cobra cardiotoxins: X-ray, NMR, and CD analysis of the effect of cis-proline conformation on three-fingered toxins.
Authors: Chen, T.S. / Chung, F.Y. / Tjong, S.C. / Goh, K.S. / Huang, W.N. / Chien, K.Y. / Wu, P.L. / Lin, H.C. / Chen, C.J. / Wu, W.G.
History
DepositionJun 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 6


Theoretical massNumber of molelcules
Total (without water)6,6991
Polymers6,6991
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.618, 39.618, 153.571
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cytotoxin 6 / Cardiotoxin VI


Mass: 6699.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: P80245
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.73 Å3/Da / Density % sol: 28.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 6473 / Num. obs: 6187 / % possible obs: 95.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.69 Å / % possible all: 87

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2807 628 RANDOM
Rwork0.239 --
all0.249 6473 -
obs0.24 6187 -
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms461 0 0 36 497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4

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