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- PDB-7x6g: Outer membrane lipoprotein QseG of Escherichia coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 7x6g
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. / Quorum-sensing regulator protein G
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)122,5376
Polymers122,5376
Non-polymers00
Water2,396133
1
A: Quorum-sensing regulator protein G
B: 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 area3610 Å2
ΔGint-38 kcal/mol
Surface area17610 Å2
MethodPISA
2
C: Quorum-sensing regulator protein G
D: 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 area3700 Å2
ΔGint-38 kcal/mol
Surface area17570 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 area3840 Å2
ΔGint-36 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.383, 149.928, 88.138
Angle α, β, γ (deg.)90.000, 95.632, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.32 M Lithium chloride, 0.1 M Sodium citrate pH 5.5, 14 % w/v PEG 4000

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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: 2.35→43.86 Å / Num. obs: 45799 / % possible obs: 98.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Net I/σ(I): 9.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4566 / CC1/2: 0.613 / Rpim(I) all: 0.549 / Rrim(I) all: 1.015 / % possible all: 99.9

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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: 2.35→37.854 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 11.891 / SU ML: 0.273 / Cross valid method: FREE R-VALUE / ESU R: 0.436 / ESU R Free: 0.295
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2964 2367 5.173 %
Rwork0.2452 43392 -
all0.248 --
obs-45759 98.223 %
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: 63.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.026 Å2-0 Å20.061 Å2
2---0.01 Å2-0 Å2
3---0.024 Å2
Refinement stepCycle: LAST / Resolution: 2.35→37.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 0 133 7434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0127436
X-RAY DIFFRACTIONr_angle_refined_deg0.6821.64510066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.95882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5122.016496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6931581
X-RAY DIFFRACTIONr_chiral_restr0.0590.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025699
X-RAY DIFFRACTIONr_nbd_refined0.1650.23238
X-RAY DIFFRACTIONr_nbtor_refined0.2870.25100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2165
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.215
X-RAY DIFFRACTIONr_mcbond_it1.3996.2573543
X-RAY DIFFRACTIONr_mcangle_it2.49.3754420
X-RAY DIFFRACTIONr_scbond_it1.6866.4253893
X-RAY DIFFRACTIONr_scangle_it2.8739.5445646
X-RAY DIFFRACTIONr_lrange_it5.62982.73511102
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
2.35-2.4110.3692110.36132630.36134790.5970.699.85630.354
2.411-2.4770.3431820.33530670.33632550.6920.71699.81570.328
2.477-2.5480.341660.30331440.30533180.7750.78999.75890.291
2.548-2.6260.3771570.29829420.30231000.7880.80799.96770.284
2.626-2.7120.3551670.29129270.29531010.790.82599.77430.276
2.712-2.8070.3491350.28827720.29129080.7990.83499.96560.269
2.807-2.9120.3251430.26427310.26728780.8590.87499.8610.244
2.912-3.030.2851250.24725970.24827290.8840.89999.74350.229
3.03-3.1640.2951460.27225110.27426650.8660.86999.69980.255
3.164-3.3170.3561230.26323810.26825250.8210.86699.16830.253
3.317-3.4950.2791070.24822460.2523760.8860.89199.0320.241
3.495-3.7050.3011400.23620890.2422870.8810.90897.46390.234
3.705-3.9580.2791160.23519370.23821570.9060.91295.17850.235
3.958-4.2710.298810.22817750.23119740.8850.91294.02230.233
4.271-4.6730.272810.20816430.21118420.9050.9393.59390.219
4.673-5.2150.299830.23714930.24116690.8870.90194.42780.25
5.215-6.0030.367550.29913380.30214840.810.85493.86790.31
6.003-7.3060.329630.25211620.25512660.8730.91296.76150.266
7.306-10.1450.194580.158510.1539660.9540.96994.09940.176
10.145-37.8540.171280.1775230.1775970.9580.96692.29480.198

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