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- PDB-2mva: Solution structure of the toxin, RhTx -

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Basic information

Entry
Database: PDB / ID: 2mva
TitleSolution structure of the toxin, RhTx
ComponentsRhTx toxin
KeywordsTOXIN
Function / homologyion channel regulator activity / toxin activity / extracellular region / Tau-scoloptoxin(04)-Sm1b
Function and homology information
Biological speciesScolopendra subspinipes (arthropod)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsHong, J. / Yang, S.
CitationJournal: To be Published
Title: Solution structure of the toxin, RhTx
Authors: Hong, J. / Yang, S.
History
DepositionSep 30, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RhTx toxin


Theoretical massNumber of molelcules
Total (without water)2,9741
Polymers2,9741
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)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide RhTx toxin


Mass: 2974.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Scolopendra subspinipes (arthropod) / References: UniProt: A0A0N7CSQ4*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

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Sample preparation

DetailsContents: 3 mM protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 3 mM / Component: entity-1
Sample conditionsIonic strength: 0.025 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardpeak picking
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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