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- PDB-5o7j: Structural insights into the periplasmic sensor domain of the Gac... -

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Basic information

Entry
Database: PDB / ID: 5o7j
TitleStructural insights into the periplasmic sensor domain of the GacS histidine kinase controlling biofilm formation in Pseudomonas aeruginosa
ComponentsHistidine kinase
KeywordsSIGNALING PROTEIN / Periplasmic detection domain / Histidine-Kinase / GacS / Biofilm
Function / homology
Function and homology information


positive regulation of secondary metabolite biosynthetic process / positive regulation of cell motility / histidine kinase / phosphorelay sensor kinase activity / plasma membrane
Similarity search - Function
Histidine kinase BarA, N-terminal / Single cache domain 4 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Histidine kinase BarA, N-terminal / Single cache domain 4 / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) 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. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
histidine kinase / histidine kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAli-Ahmad, A. / Bornet, O. / Fadel, F. / Bourne, Y. / Vincent, F. / Guerlesquin, F. / Sebban-Kreuzer, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Sci Rep / Year: 2017
Title: Structural and functional insights into the periplasmic detector domain of the GacS histidine kinase controlling biofilm formation in Pseudomonas aeruginosa.
Authors: Ali-Ahmad, A. / Fadel, F. / Sebban-Kreuzer, C. / Ba, M. / Pelissier, G.D. / Bornet, O. / Guerlesquin, F. / Bourne, Y. / Bordi, C. / Vincent, F.
History
DepositionJun 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine kinase


Theoretical massNumber of molelcules
Total (without water)16,3751
Polymers16,3751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9710 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Histidine kinase /


Mass: 16375.362 Da / Num. of mol.: 1 / Fragment: periplasmic detection domain, UNP residues 54-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: gacS, PAMH19_4268 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A8RMX6, UniProt: G3XD98*PLUS, histidine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
142isotropic13D 1H-15N NOESY
152isotropic23D HNHA
161isotropic12D 1H-15N HSQC
172isotropic12D 1H-13C HSQC
182isotropic23D HNCO
192isotropic23D HCACO
1102isotropic23D HNCA
1142isotropic23D HN(CO)CA
1132isotropic23D HN(CA)CB
1122isotropic23D CBCA(CO)NH
1112isotropic23D (H)CCH-TOCSY
1162isotropic23D 1H-13C NOESY
1152isotropic23D 1H-13C NOESY aromatic
1172isotropic12D CBCACO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-99% 15N] GacS periplasmic detection domain, 150 mM sodium chloride, 50 mM sodium phosphate, 90% H2O/10% D2O15N_GacS90% H2O/10% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] GacS periplasmic detection domain, 50 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O13N-15N_GacS90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMGacS periplasmic detection domain[U-99% 15N]1
150 mMsodium chloridenatural abundance1
50 mMsodium phosphatenatural abundance1
0.8 mMGacS periplasmic detection domain[U-99% 13C; U-99% 15N]2
50 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 0.2 M / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian Uniform NMR SystemVarianUniform NMR System8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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