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- PDB-1ffj: NMR STRUCTURE OF CARDIOTOXIN IN DPC-MICELLE -

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Basic information

Entry
Database: PDB / ID: 1ffj
TitleNMR STRUCTURE OF CARDIOTOXIN IN DPC-MICELLE
ComponentsCYTOTOXIN 2
KeywordsTOXIN / all-beta sheet protein / membrane perturbation
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
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 oxiana (Central Asian cobra)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDubovskii, P.V. / Dementieva, D.V. / Bocharov, E.V. / Utkin, Y.N. / Arseniev, A.S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Membrane binding motif of the P-type cardiotoxin.
Authors: Dubovskii, P.V. / Dementieva, D.V. / Bocharov, E.V. / Utkin, Y.N. / Arseniev, A.S.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: Two forms of Cytotoxin II (cardiotoxin) from Naja naja oxiana in Aqueous Solution. Spatial Structures with Tightly Bound Water Molecules
Authors: Dementieva, D.V. / Bocharov, E.V. / Arseniev, A.S.
History
DepositionJul 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: CYTOTOXIN 2


Theoretical massNumber of molelcules
Total (without water)6,6481
Polymers6,6481
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 220target function
RepresentativeModel #1fewest violations

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Components

#1: Protein CYTOTOXIN 2 / CARDIOTOXIN


Mass: 6648.238 Da / Num. of mol.: 1 / Fragment: 1 / Source method: isolated from a natural source / Source: (natural) Naja oxiana (Central Asian cobra) / Secretion: VENOM / References: UniProt: P01441
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
131DQF-COSY
141ROESY
152DQF-COSY
1622D NOESY
172TOCSY
281ROESY
291DQF-COSY
21012D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques. Sites of tightly bound water molecules were determined as in Dementieva et al., Eur.J.Biochem.1999,263,152-162.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM Cardiotoxin (cytotoxin II); 120 mM perdeuterated dodecylphosphocholine90% H2O/10% D2O
23mM Cardiotoxin (cytotoxin II); 120 mM perdeuterated dodecylphosphocholine100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10M NaCl 5.5ambient 318 K
20M NaCl 5.5ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1AVarian softwarecollection
XEASY1.2.11Xia, T. & Bartels, C.data analysis
DYANA1.5Guentert, P. & Mumenthaler, C.structure solution
DYANA1.5Guentert, P. & Mumenthaler, C.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: structures are based on a total of 368 NOE-derived constraints, 154 dihedral angle restraints, 248 distance restraints from hydrogen bonds and disulfides
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 220 / Conformers submitted total number: 20

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