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- PDB-9m06: Outer membrane lipoprotein QseG of Salmonella enterica serovar Ty... -

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Basic information

Entry
Database: PDB / ID: 9m06
TitleOuter membrane lipoprotein QseG of Salmonella enterica serovar Typhimurium SL1344
ComponentsOuter membrane lipoprotein
KeywordsSIGNALING PROTEIN / signal activation
Function / homologyQuorum-sensing regulator protein G / YfhG lipoprotein / ACETATE ION / DI(HYDROXYETHYL)ETHER / Hypothetical membrane protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane lipoprotein
B: Outer membrane lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8727
Polymers42,5302
Non-polymers3425
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-36 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 41.001, 126.658
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Outer membrane lipoprotein / Two-component system QseEF-associated lipoprotein QseG


Mass: 21265.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Gene: yfhG, qseG, SL1344_2525, G1W50_19190, G1W53_19070, G1W54_19660, G1W56_19535, G1W63_19335, G1W64_19365, G1W86_18045, G1W87_18985, G1W89_18830, G1W92_18735, G1X03_18695, G1X04_08460, G1X09_19680, ...Gene: yfhG, qseG, SL1344_2525, G1W50_19190, G1W53_19070, G1W54_19660, G1W56_19535, G1W63_19335, G1W64_19365, G1W86_18045, G1W87_18985, G1W89_18830, G1W92_18735, G1X03_18695, G1X04_08460, G1X09_19680, G1X10_19590, G1X13_19670, G1X17_20470, G1X23_19065, G1X29_19380, G1X32_19630, G1X38_19925, G1X42_18740, G1X47_19355, G1X49_18700, G1X51_19680, G1X52_19370, G1X66_19045, G1X68_16400, G1X69_19950, G1X71_19685, G1X76_19340, G1X80_18180, G1X84_18735, G1X85_19495, G1X86_19670, G1X94_19190, G1X96_19675, G1X99_19370, G1Y02_19370
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3NKH9
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) PEG8000, 0.1 M sodium cacodylate pH 6.7, 0.2 M magnesium acetate

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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: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26629 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 0.977 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 2506 / CC1/2: 0.754

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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: 2.1→37.14 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 3112 7.7 %
Rwork0.2102 37281 -
obs0.212 25894 77.8 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 23 189 2508
LS refinement shellResolution: 2.1→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3292 60 -
Rwork0.3203 721 -
obs--33 %

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