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- PDB-2m35: NMR study of k-Ssm1a -

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Basic information

Entry
Database: PDB / ID: 2m35
TitleNMR study of k-Ssm1a
Componentsk-Ssm1a
KeywordsTOXIN / Kv1.3 / Potassium channel / Centipede / Blocker
Function / homologyDiphtheria Toxin Repressor; domain 2 - #50 / Diphtheria Toxin Repressor; domain 2 / toxin activity / Orthogonal Bundle / extracellular region / Mainly Alpha / Kappa-scoloptoxin(03)-Ssm1a
Function and homology information
Biological speciesScolopendra subspinipes (arthropod)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsHighest molprobity percentile, model1
AuthorsKing, G.F. / Undheim, E.A. / Mobli, M. / Yang, S. / Rong, M. / Lai, R.
CitationJournal: To be Published
Title: NMR study of k-Ssm1a
Authors: Undheim, E.A. / Yang, S. / Mobli, M. / Rong, M. / Lai, R. / King, G.F.
History
DepositionJan 9, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _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: k-Ssm1a


Theoretical massNumber of molelcules
Total (without water)6,2151
Polymers6,2151
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)20 / 30target function
RepresentativeModel #1highest molprobity percentile

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Components

#1: Protein k-Ssm1a


Mass: 6214.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scolopendra subspinipes (arthropod) / Plasmid: pLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: I6RU32*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D HBHA(CO)NH
1614D HCC(CO)NH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
NMR detailsText: All 3D data except for NOESY data were acquired using non-uniform sampling and processed using maximum entropy reconstruction method.

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Sample preparation

DetailsContents: 20 mM ammonium acetate, 400 uM [U-13C; U-15N] kSs1a, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMammonium acetate-11
400 uMkSs1a-2[U-13C; U-15N]1
5 %D2O-31
Sample conditionspH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XEASY3.2Bartels et al.peak picking
XEASY3.2Bartels et al.chemical shift assignment
TALOSTALOS+Cornilescu, Delaglio and Baxchemical shift calculation
TALOSTALOS+Cornilescu, Delaglio and Baxgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
Rowland_NMR_Toolkit3University of Connecticutprocessing
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1339 / NOE intraresidue total count: 350 / NOE long range total count: 228 / NOE medium range total count: 416 / NOE sequential total count: 345 / Disulfide bond constraints total count: 18 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 46
NMR representativeSelection criteria: highest molprobity percentile
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 30 / Conformers submitted total number: 20

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