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- PDB-7o2k: NMR solution structue of cytotoxin 2 from Naja Kaouthia -

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Basic information

Entry
Database: PDB / ID: 7o2k
TitleNMR solution structue of cytotoxin 2 from Naja Kaouthia
ComponentsCytotoxin 2
KeywordsTOXIN / S-type cytotoxin / cobra venom / three-finger protein / membrane-active polypeptide
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 / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesNaja kaouthia (monocled cobra)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDubinnyi, M.A. / Dubovskii, P.V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: The omega-loop of cobra cytotoxins tolerates multiple amino acid substitutions.
Authors: Dubinnyi, M.A. / Dubovskii, P.V. / Starkov, V.G. / Utkin, Y.N.
History
DepositionMar 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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

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Assembly

Deposited unit
A: Cytotoxin 2


Theoretical massNumber of molelcules
Total (without water)6,7561
Polymers6,7561
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4170 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Cytotoxin 2 / CX2 / Toxin CM-7A


Mass: 6756.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P01445
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D TOCSY
131isotropic22D NOESY
141isotropic12D 1H-1H COSY
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-15N HSQC
171isotropic12D 1H-13C HSQC-TOCSY

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Sample preparation

DetailsType: solution
Contents: 2 mM cytotoxin 2, 3 mM Cytotoxin 3, 90% H2O/10% D2O
Details: 3 mM No Cytotoxin 3 from Naja kaouthia, 2 mM No Cytotoxin 2 from Naja kaouthia, 90% H2O/10% D2O
Label: The mixture of CT3 and CT2 Naja kaouthia / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMcytotoxin 2natural abundance1
3 mMCytotoxin 3natural abundance1
Sample conditionsIonic strength: 0 mM / Ionic strength err: 0 / Label: Cytotoxins 2 and 3 / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 303 K / Temperature err: 1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert P.refinement
CYANA1.0.3Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 582 NOE constraints, 109 angular constraints, 27 H-bonds, 4 SS-bonds
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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