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- PDB-1je9: NMR SOLUTION STRUCTURE OF NT2 -

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Basic information

Entry
Database: PDB / ID: 1je9
TitleNMR SOLUTION STRUCTURE OF NT2
ComponentsSHORT NEUROTOXIN II
KeywordsTOXIN / all beta sheet protein / postsynaptic neurotoxin / veonm
Function / homology
Function and homology information


host cell postsynaptic membrane / : / toxin activity / extracellular region
Similarity search - Function
Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja kaouthia (monocled cobra)
MethodSOLUTION NMR / Simulated annealing, molecular dynamics
AuthorsCheng, Y. / Wang, W. / Wang, J.
CitationJournal: BIOCHIM.BIOPHYS.ACTA / Year: 2002
Title: Structure-function relationship of three neurotoxins from the venom of Naja kaouthia: a comparison between the NMR-derived structure of NT2 with its homologues, NT1 and NT3
Authors: Cheng, Y. / Meng, Q. / Wang, W. / Wang, J.
History
DepositionJun 16, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 4, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHORT NEUROTOXIN II


Theoretical massNumber of molelcules
Total (without water)6,8701
Polymers6,8701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SHORT NEUROTOXIN II / SHORT NEUROTOXIN 1 - MONOCLED COBRA


Mass: 6869.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: P59276

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131E-COSY
1412D TOCSY

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Sample preparation

DetailsContents: 4mM NT2 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.0 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98MSIdata analysis
XwinNMR1BRUKERcollection
CNS1A.T. Brungerstructure solution
CNS1A.T. Brungerrefinement
RefinementMethod: Simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 18

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