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- PDB-2kb1: NMR studies of a channel protein without membrane: structure and ... -

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Basic information

Entry
Database: PDB / ID: 2kb1
TitleNMR studies of a channel protein without membrane: structure and dynamics of water-solubilized KcsA
ComponentsWSK3
KeywordsMEMBRANE PROTEIN / protein / homotetramer
Function / homologyHelix Hairpins - #70 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsEntry contains 20 NMR structures calculated and refined using xplor-nih without further ...Entry contains 20 NMR structures calculated and refined using xplor-nih without further minimization in water box
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. / Tang, P. / Meirovitch, E. / Eckenhoff, R. / Carnini, A. / Xu, Y.
History
DepositionNov 19, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 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 22, 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: WSK3
B: WSK3
C: WSK3
D: WSK3


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

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Components

#1: Protein
WSK3


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: Entry contains 20 NMR structures calculated and refined using xplor-nih without further minimization in water box
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
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipe2.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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