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- PDB-2k1e: NMR studies of a channel protein without membranes: structure and... -

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Basic information

Entry
Database: PDB / ID: 2k1e
TitleNMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA
Componentswater soluble analogue of potassium channel, KcsA
KeywordsMEMBRANE PROTEIN / homotetramer / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homologyHelix Hairpins - #70 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailswater soluble analogue of potassium channel, KcsA
AuthorsMa, D. / Xu, Y. / Tillman, T. / Tang, P. / Meirovitch, E. / Eckenhoff, R. / Carnini, A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: NMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA.
Authors: Ma, D. / Tillman, T.S. / Tang, P. / Meirovitch, E. / Eckenhoff, R. / Carnini, A. / Xu, Y.
History
DepositionFeb 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: water soluble analogue of potassium channel, KcsA
B: water soluble analogue of potassium channel, KcsA
C: water soluble analogue of potassium channel, KcsA
D: water soluble analogue of potassium channel, KcsA


Theoretical massNumber of molelcules
Total (without water)45,6194
Polymers45,6194
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
water soluble analogue of potassium channel, KcsA


Mass: 11404.628 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: designed variant of KcsA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: water soluble analogue of potassium channel, KcsA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D (H)CCH-TOCSY
171T1, T2, hetNOE
181R2 dispersion
191diffusion measurement

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-15N] WSK3_15N, 55 M [U-2H] D2O, 0.2 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.2 mM [U-13C; U-15N] WSK3, 55 M [U-2H] D2O, 0.2 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMWSK3_15N[U-15N]1
55 MD2O[U-2H]1
0.2 mMDSS1
0.2 mMwsk3[U-13C; U-15N]2
55 MD2O[U-2H]2
0.2 mMDSS2
Sample conditionsIonic strength: no salt / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
TopSpin1.3Bruker Biospincollection
Sparky3.11Goddarddata analysis
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XPLOR_NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure is further refined with energy minimization in water box without NMR constraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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