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- PDB-9m07: Histidine kinase QseE sensor domain of Salmonella Typhimurium SL1344 -

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Basic information

Entry
Database: PDB / ID: 9m07
TitleHistidine kinase QseE sensor domain of Salmonella Typhimurium SL1344
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / Histidine kinase
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / ATP binding / plasma membrane
Similarity search - Function
: / Histidine kinase/HSP90-like ATPase / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...: / Histidine kinase/HSP90-like ATPase / 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGao, X. / Li, G.B. / Gong, P.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200144 China
CitationJournal: Mbio / Year: 2025
Title: Cryo-EM structure of the QseG-QseE complex reveals an accessory protein-driven two-component system activation mechanism
Authors: Gao, X. / Li, G.B. / Gong, P.Q.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: histidine kinase


Theoretical massNumber of molelcules
Total (without water)14,9851
Polymers14,9851
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.452, 55.452, 86.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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Components

#1: Protein histidine kinase


Mass: 14984.701 Da / Num. of mol.: 1 / Fragment: QseE sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Gene: G1W55_21660, G1W57_21075, G1W59_09275, G1W66_20535, G1W69_20505, G1W71_21505, G1W72_11380, G1W73_10360, G1W74_21080, G1W84_13470, G1W85_13465, G1W99_23435, G1X00_13645, G1X06_20175, G1X11_ ...Gene: G1W55_21660, G1W57_21075, G1W59_09275, G1W66_20535, G1W69_20505, G1W71_21505, G1W72_11380, G1W73_10360, G1W74_21080, G1W84_13470, G1W85_13465, G1W99_23435, G1X00_13645, G1X06_20175, G1X11_11700, G1X12_12075, G1X15_13125, G1X18_13650, G1X19_12300, G1X27_11005, G1X31_13200, G1X35_19325, G1X41_12250, G1X46_12430, G1X54_21230, G1X75_21695, G1X77_21670, G1X98_13465
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A719LJQ8, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 3.5 M Sodium formate, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 5687 / % possible obs: 99.9 % / Redundancy: 23.5 % / Biso Wilson estimate: 33.12 Å2 / CC1/2: 0.992 / Net I/σ(I): 30
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 541 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25.49 Å / SU ML: 0.303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2747 537 10.02 %
Rwork0.2226 4823 -
obs0.2279 5360 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 0 31 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033854
X-RAY DIFFRACTIONf_angle_d0.58281151
X-RAY DIFFRACTIONf_chiral_restr0.0333131
X-RAY DIFFRACTIONf_plane_restr0.0062152
X-RAY DIFFRACTIONf_dihedral_angle_d3.7467122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.33341080.2652987X-RAY DIFFRACTION79.69
2.64-3.020.32551380.25641233X-RAY DIFFRACTION99.49
3.02-3.810.24741400.22131250X-RAY DIFFRACTION99.64
3.81-25.490.25981510.20141353X-RAY DIFFRACTION99.67

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