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- PDB-1wm7: Solution Structure of BmP01 from the Venom of Scorpion Buthus mar... -

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Basic information

Entry
Database: PDB / ID: 1wm7
TitleSolution Structure of BmP01 from the Venom of Scorpion Buthus martensii Karsch, 9 structures
ComponentsNeurotoxin BmP01
KeywordsTOXIN / ALPHA/BETA scaffold
Function / homologyShort scorpion toxin, potassium channel inhibitor alpha-KTx 8/9 / BmTXKS1/BmP02 toxin family / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / : / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 8.2
Function and homology information
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodSOLUTION NMR / distance geometry
AuthorsWu, G. / Li, Y. / Wei, D. / He, F. / Jiang, S. / Hu, G. / Wu, H. / Chen, X.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2000
Title: Solution Structure of BmP01 from the Venom of Scorpion Buthus martensii Karsch
Authors: Wu, G. / Li, Y. / Wei, D. / He, F. / Jiang, S. / Hu, G. / Wu, H.
History
DepositionJul 5, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

Downloads & links

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Assembly

Deposited unit
A: Neurotoxin BmP01


Theoretical massNumber of molelcules
Total (without water)3,1891
Polymers3,1891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Neurotoxin BmP01 / Potassium ion channel blocker P01


Mass: 3188.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / References: UniProt: Q9U8D2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY, 2D TOCSY, DQF-COSY
2212D NOESY, 2D TOCSY
1322D NOESY, 2D TOCSY, DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.25mM90% H2O/10% D2O
23.25mM100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.0 ambient 303 K
23.0 ambient 313 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BMike Carlisle, Dan Steele, Mike Millercollection
VNMR6.1BMike Carlisle, Dan Steele, Mike Millerprocessing
Sybyl(triadNMR model)6.3Tripos, Inc.data analysis
Sybyl(DIANA program)6.3Tripos, Inc.structure solution
SYBYL6.3Tripos, Inc.refinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: the structure are based on a total of 381 constraints, 337 are NOE-derived distance constraints,21 dihedral angle constraints,23 distance constraints from seven hydrogen bonds and three disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 9

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