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- PDB-1ccq: NMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II ... -

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Basic information

Entry
Database: PDB / ID: 1ccq
TitleNMR STRUCTURE WITH TIGHTLY BOUND WATER MOLECULES OF CYTOTOXIN II (CARDIOTOXIN) FROM NAJA NAJA OXIANA IN AQUEOUS SOLUTION (MINOR FORM).
ComponentsPROTEIN (CYTOTOXIN 2)
KeywordsTOXIN / CYTOTOXIN (CARDIOTOXIN) / MEMBRANE PERTURBATION / CIS/TRANS ISOMERIZATION / BOUND WATER
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 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
Biological speciesNaja oxiana (Central Asian cobra)
MethodSOLUTION NMR / SIMULATED ANNEALING BY MOLECULAR DYNAMICS IN TORSION ANGLE SPACE
AuthorsDementieva, D.V. / Bocharov, E.V. / Arseniev, A.S.
Citation
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.
#1: Journal: RUSS.J.BIOORGANIC CHEM. / Year: 1996
Title: Secondary Structure and Conformational Heterogeneity of Cytotoxin II from Naja Naja Oxiana
Authors: Dementieva, D.V. / Utkin Yu, N. / Arseniev, A.S.
History
DepositionMar 2, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Revision 1.4Dec 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 1.5Nov 6, 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: PROTEIN (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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 220LEAST RESTRAINT VIOLATION (TARGET FUNCTION VALUE)
Representative

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Components

#1: Protein PROTEIN (CYTOTOXIN 2)


Mass: 6648.238 Da / Num. of mol.: 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
111COSY
121TOCSY
131NOESY
141ROESY
NMR detailsText: THE STRUCTURE WAS DETERMINED BY HOMONUCLEAR NMR SPECTROSCOPY, USING GRADIENT TECHNIQUE. ROESY EXPERIMENTS WERE HELD AT 290 AND 318K.

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Sample preparation

DetailsContents: 90% WATER/10% D2O, 100% D2O
Sample conditionspH: 5.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
FANTOM4FRACZKIEWICZ, MUMENTHALER, FREYBERG, SCHAUMANNrefinement
VARIAN VNMRVNMRstructure solution
XEASYstructure solution
DYANAstructure solution
RefinementMethod: SIMULATED ANNEALING BY MOLECULAR DYNAMICS IN TORSION ANGLE SPACE
Software ordinal: 1
Details: THE RESTRAINED REFINMENT WAS MADE IN VACUUM AND ONLY FOR PROTEIN SIDE CHAINS.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION (TARGET FUNCTION VALUE)
Conformers calculated total number: 220 / Conformers submitted total number: 20

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