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

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Basic information

Entry
Database: PDB / ID: 2ksd
TitleBackbone structure of the membrane domain of E. coli histidine kinase receptor ArcB, Center for Structures of Membrane Proteins (CSMP) target 4310C
ComponentsAerobic respiration control sensor protein arcB
KeywordsTRANSFERASE / methods development / Histidine kinase receptor / membrane domain / two-helical hairpin / cell-free synthesis / Cell inner membrane / Cell membrane / Kinase / Transcription / Transcription regulation / 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


response to oxygen levels / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily ...His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Aerobic respiration control sensor protein ArcB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsMaslennikov, I. / Klammt, C. / Hwang, E. / Kefala, G. / Kwiatkowski, W. / Jeon, Y. / 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 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerobic respiration control sensor protein arcB


Theoretical massNumber of molelcules
Total (without water)13,3041
Polymers13,3041
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Aerobic respiration control sensor protein arcB


Mass: 13303.974 Da / Num. of mol.: 1 / Fragment: N-terminal residues 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: arcB, b3210, JW5536 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: P0AEC3, 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
1222D 1H-15N HSQC
1313D 1H-15N NOESY
1423D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM DSS, 20 mM sodium acetate, 200 mM 1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)], 10 mM sodium chloride, 0.5 mM [U-98% 13C; U-98% 15N] Protein, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM DSS, 100 mM 1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)], 20 mM Mes-BisTris, 0.3 mM [U-99% 13C; U-99% 15N] Protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDSS-11
20 mMsodium acetate-21
200 mM1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]-31
10 mMsodium chloride-41
0.5 mMProtein-5[U-98% 13C; U-98% 15N]1
0.5 mMDSS-62
100 mM1-myristoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)]-72
20 mMMes-BisTris-82
0.3 mMProtein-9[U-99% 13C; U-99% 15N]2
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker AvanceBrukerAvance7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guntert, Mumenthaler and Wuthrichstructure solution
TOPSPIN2.1Bruker Biospincollection
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichdata analysis
Molmol2K.2Koradi, Billeter and Wuthrichstructure visualization and analysis
CYANA1.0.6Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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