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- PDB-2ksf: Backbone structure of the membrane domain of E. coli histidine ki... -

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Basic information

Entry
Database: PDB / ID: 2ksf
TitleBackbone structure of the membrane domain of E. coli histidine kinase receptor KdpD, Center for Structures of Membrane Proteins (CSMP) target 4312C
ComponentsSensor protein kdpD
KeywordsTRANSFERASE / methods development / Histidine kinase receptor / membrane domain / four-helical bundle / cell-free synthesis / ATP-binding / Cell inner membrane / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Transmembrane / Two-component regulatory system / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / cellular response to potassium ion / histidine kinase / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / signal transduction / protein homodimerization activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Backbone structure of the membrane domain of e. Coli histidine kinase receptor kdpd, / : / Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Backbone structure of the membrane domain of e. Coli histidine kinase receptor kdpd, / : / Signal transduction histidine kinase, osmosensitive K+ channel sensor, N-terminal / Sensor protein KdpD, transmembrane domain / KdpD, transmembrane domain superfamily / Osmosensitive K+ channel His kinase sensor domain / Domain of unknown function (DUF4118) / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / GAF-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsMaslennikov, I. / Klammt, C. / Kefala, G. / Okamura, M. / Esquivies, L. / Kwiatkowski, W. / Choe, S. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis.
Authors: Maslennikov, I. / Klammt, C. / Hwang, E. / Kefala, G. / Okamura, M. / Esquivies, L. / Mors, K. / Glaubitz, C. / Kwiatkowski, W. / Jeon, Y.H. / Choe, S.
History
DepositionJan 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein kdpD


Theoretical massNumber of molelcules
Total (without water)11,4431
Polymers11,4431
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sensor protein kdpD


Mass: 11442.651 Da / Num. of mol.: 1 / Fragment: sequence database residues 397-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0695, JW0683, kdpD / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P21865, histidine kinase

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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 HNCO
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.5 mM DSS, 20 mM Mes-BisTris, 100 mM 1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)], 0.3 mM [U-99% 13C; U-99% 15N] Protein, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDSS-11
20 mMMes-BisTris-21
100 mM1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]-31
0.3 mMProtein-4[U-99% 13C; U-99% 15N]1
Sample conditionspH: 6 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guntert, Mumenthaler and Wuthrichstructure solution
CARA2K.2Keller and Wuthrichdata analysis
CARA2K.2Keller and Wuthrichpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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