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- PDB-1pvz: Solution Structure of BmP07, A Novel Potassium Channel Blocker fr... -

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Basic information

Entry
Database: PDB / ID: 1pvz
TitleSolution Structure of BmP07, A Novel Potassium Channel Blocker from Scorpion Buthus martensi Karsch, 15 structures
ComponentsK+ toxin-like peptide
KeywordsTOXIN / ALPHA/BETA scaffold
Function / homologyKnottin, scorpion toxin-like superfamily / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 14.2
Function and homology information
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodSOLUTION NMR / distance geometry
AuthorsWu, H. / Zhang, N. / Wang, Y. / Zhang, Q. / Ou, L. / Li, M. / Hu, G.
CitationJournal: PROTEINS / Year: 2004
Title: Solution structure of BmKK2, a new potassium channel blocker from the venom of chinese scorpion Buthus martensi Karsch
Authors: Zhang, N. / Li, M. / Chen, X. / Wang, Y. / Wu, G. / Hu, G. / Wu, H.
History
DepositionJun 29, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly ...citation_author / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: K+ toxin-like peptide


Theoretical massNumber of molelcules
Total (without water)3,2531
Polymers3,2531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide K+ toxin-like peptide / scorpion neurotoxin / BmP07


Mass: 3252.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / References: UniProt: Q95NK7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
1312D TOCSY
142DQF-COSY
1522D NOESY
1622D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.7mM BmP07; 90% H2O, 10% D2O90% H2O/10% D2O
22.7mM BmP07; 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13ambient 300 K
22.6ambient 300 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
XEASY1994Tai-he Xia, Christian Barteldata analysis
DYANA1.5Peter Guntert, Christian Mumenthaler, Torsten Herrmannstructure solution
AMBER5Peter Kollman, Dave Case, Ken Merz, Thomas Cheatham, Carlos Simmerling, Vertex Pharmaceuticalsrefinement
RefinementMethod: distance geometry / Software ordinal: 1
Details: the structures are based on a total of 277 constraints, 249 are NOE-derived distance constraints, 9 dihedral angle constraints, 19 distance constraints from five hydrogen bonds and three disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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