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- PDB-7x6f: Outer membrane lipoprotein QseG of Escherichia coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 7x6f
TitleOuter membrane lipoprotein QseG of Escherichia coli O157:H7
ComponentsQuorum-sensing regulator protein G
KeywordsSIGNALING PROTEIN / Enterohemorrhagic Escherichia coli / Two-component systems / Outer membrane lipoprotein
Function / homologyQuorum-sensing regulator protein G / YfhG lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / CITRATE ANION / SERINE / Quorum-sensing regulator protein G
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMatsumoto, K. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structures of QseE and QseG: elements of a three-component system from Escherichia coli.
Authors: Matsumoto, K. / Fukuda, Y. / Inoue, T.
History
DepositionMar 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quorum-sensing regulator protein G
B: Quorum-sensing regulator protein G
C: Quorum-sensing regulator protein G
D: Quorum-sensing regulator protein G
E: Quorum-sensing regulator protein G
F: Quorum-sensing regulator protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,40516
Polymers122,5376
Non-polymers86810
Water5,026279
1
A: Quorum-sensing regulator protein G
B: Quorum-sensing regulator protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1316
Polymers40,8462
Non-polymers2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-39 kcal/mol
Surface area17940 Å2
MethodPISA
2
C: Quorum-sensing regulator protein G
D: Quorum-sensing regulator protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4288
Polymers40,8462
Non-polymers5836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-44 kcal/mol
Surface area17860 Å2
MethodPISA
3
E: Quorum-sensing regulator protein G
F: Quorum-sensing regulator protein G


Theoretical massNumber of molelcules
Total (without water)40,8462
Polymers40,8462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-36 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.963, 149.785, 88.302
Angle α, β, γ (deg.)90.000, 94.649, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Quorum-sensing regulator protein G


Mass: 20422.787 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: qseG, yfhG, Z3831, ECs3421 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AD45

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Non-polymers , 6 types, 289 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.08 M magnesium acetate tetrahydrate, 0.1 M sodium citrate pH 6.0, 14% (w/v) polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→43.43 Å / Num. obs: 48807 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4582 / CC1/2: 0.65 / Rpim(I) all: 0.516 / Rrim(I) all: 0.983 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold structure

Resolution: 2.3→39.803 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: FREE R-VALUE / ESU R: 0.366 / ESU R Free: 0.262
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2735 2466 5.056 %
Rwork0.2206 46308 -
all0.223 --
obs-48774 98.839 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.887 Å2
Baniso -1Baniso -2Baniso -3
1--0.095 Å20 Å2-0.031 Å2
2---0.006 Å2-0 Å2
3---0.105 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7281 0 57 279 7617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0127555
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.64610227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3325895
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12221.885504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.163151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351584
X-RAY DIFFRACTIONr_chiral_restr0.0650.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025824
X-RAY DIFFRACTIONr_nbd_refined0.230.23465
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2450.2317
X-RAY DIFFRACTIONr_metal_ion_refined0.0190.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.2174
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.213
X-RAY DIFFRACTIONr_mcbond_it5.6065.0413578
X-RAY DIFFRACTIONr_mcangle_it6.6257.5254471
X-RAY DIFFRACTIONr_scbond_it7.5345.423977
X-RAY DIFFRACTIONr_scangle_it9.1067.9215756
X-RAY DIFFRACTIONr_lrange_it9.30567.22811600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.2631600.16934750.17336470.8680.91299.6710.168
2.36-2.4240.2431740.17533440.17935220.8960.91899.88640.171
2.424-2.4940.2391720.18432720.18734460.8990.91699.9420.178
2.494-2.570.2851630.18231680.18733400.8730.91299.73050.172
2.57-2.6540.2371380.18430980.18632360.9120.921000.175
2.654-2.7470.2291700.20329670.20431410.9090.91899.87270.194
2.747-2.850.2781670.20928590.21330360.8960.9199.67060.196
2.85-2.9660.2671360.22127280.22328770.8870.999.54810.209
2.966-3.0970.3041280.23226610.23528040.8660.88999.4650.218
3.097-3.2470.2931510.2324960.23426710.8650.999.10150.217
3.247-3.4220.31260.23423770.23725400.8820.90498.54330.226
3.422-3.6280.281120.23522860.23724380.8880.91298.35930.228
3.628-3.8760.2441120.22920730.2322590.910.91296.72420.225
3.876-4.1830.2821070.22219120.22520890.8850.92396.64910.225
4.183-4.5770.268900.20718090.20919610.9020.93196.83830.215
4.577-5.1090.2671060.22116010.22417490.9110.91697.59860.241
5.109-5.8830.341010.28814330.29115690.8630.88397.76930.306
5.883-7.1660.301730.27712460.27913480.8730.87997.84870.3
7.166-9.9740.266620.29280.20410330.9010.94195.83740.234
9.974-39.8030.187180.225750.2196180.960.94195.95470.258

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