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- PDB-2mj6: Solution structure of the extracellular sensor domain of DraK his... -

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Basic information

Entry
Database: PDB / ID: 2mj6
TitleSolution structure of the extracellular sensor domain of DraK histidine kinase
ComponentsPutative two-component system histidine kinaseTwo-component regulatory system
KeywordsTRANSFERASE / DraK / Histidine Kinase
Function / homology
Function and homology information


regulation of response to osmotic stress / histidine kinase / phosphorelay sensor kinase activity / plasma membrane => GO:0005886
Similarity search - Function
Beta-Lactamase - #250 / Histidine kinase DraK, N-terminal domain / DraK Histidine Kinase N-terminal domain / HAMP domain profile. / HAMP domain / 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 ...Beta-Lactamase - #250 / Histidine kinase DraK, N-terminal domain / DraK Histidine Kinase N-terminal domain / HAMP domain profile. / HAMP domain / 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. / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsYeo, K. / Cheong, H.
CitationJournal: Plos One / Year: 2014
Title: Mechanism of the pH-Induced Conformational Change in the Sensor Domain of the DraK Histidine Kinase via the E83, E105, and E107 Residues
Authors: Yeo, K.J. / Hong, Y.S. / Jee, J.G. / Lee, J.K. / Kim, H.J. / Park, J.W. / Kim, E.H. / Hwang, E. / Kim, S.Y. / Lee, E.G. / Kwon, O. / Cheong, H.K.
History
DepositionDec 25, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 24, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative two-component system histidine kinase


Theoretical massNumber of molelcules
Total (without water)9,7611
Polymers9,7611
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative two-component system histidine kinase / Two-component regulatory system / DraK


Mass: 9760.796 Da / Num. of mol.: 1 / Fragment: UNP residues 28-115 / Mutation: E83Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO3062 / Production host: Streptomyces coelicolor (bacteria) / References: UniProt: Q9KZ83

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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 CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-13C NOESY
1813D 1H-15N NOESY
1913D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.8 mM [U-13C; U-15N] DraK-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: DraK-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0.05 / pH: 4.5 / 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
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
Amberrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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