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- PDB-2kbk: Solution Structure of BmK-M10 -

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Basic information

Entry
Database: PDB / ID: 2kbk
TitleSolution Structure of BmK-M10
ComponentsNeurotoxin BmK-M10
KeywordsTOXIN / protein / Ionic channel inhibitor / Neurotoxin / Secreted / Sodium channel inhibitor
Function / homology
Function and homology information


potassium channel inhibitor activity / sodium channel inhibitor activity / : / defense response / toxin activity / extracellular region
Similarity search - Function
Scorpion long chain toxin / LCN-type cysteine-stabilized alpha/beta (CS-alpha/beta) domain profile. / Scorpion long chain toxin/defensin / Scorpion toxin-like domain / Knottins / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMesobuthus martensii (Chinese scorpion)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsZhu, J. / Wu, H.
CitationJournal: To be Published
Title: Solution Structure of BmK-M10
Authors: Zhu, J. / Tong, X. / Cao, C. / Wu, H.
History
DepositionNov 28, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 11, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: pdbx_nmr_sample_details / pdbx_nmr_software ...pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
Item: _pdbx_nmr_sample_details.contents / _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 BmK-M10


Theoretical massNumber of molelcules
Total (without water)7,0551
Polymers7,0551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Neurotoxin BmK-M10 / BmK-X / BmKX / BmK10 / Bmk M10 / BmkM10 / Neurotoxin M10 / Alpha-neurotoxin TX9 / BmKalphaTx9 / BmK AngM1


Mass: 7055.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Buthus martensii Karsch / Source: (natural) Mesobuthus martensii (Chinese scorpion) / References: UniProt: O61705

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D DQF-COSY
1312D 1H-1H NOESY
2412D 1H-1H TOCSY
2512D DQF-COSY
2612D 1H-1H NOESY
1722D 1H-1H TOCSY
1822D DQF-COSY
1922D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.9 mM BmK-M10, 90% H2O/10% D2O90% H2O/10% D2O
21.9 mM BmK-M10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.9 mMBmK-M101
1.9 mMBmK-M102
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 4.34 ambient 298 K
220 5.52 ambient 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
VNMRVariandata analysis
VNMRVarianprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthurstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
ProcheckNMRLaskowski and MacArthurrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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