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- PDB-7x6h: Outer membrane lipoprotein QseG of Escherichia coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 7x6h
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: 2.6 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


Theoretical massNumber of molelcules
Total (without water)81,6914
Polymers81,6914
Non-polymers00
Water77543
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 area3850 Å2
ΔGint-42 kcal/mol
Surface area18540 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 area3840 Å2
ΔGint-40 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.087, 123.808, 150.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Quorum-sensing regulator protein G


Mass: 20422.787 Da / Num. of mol.: 4
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.: 43 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 13 % w/v PEG 8000

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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: 2.6→47.76 Å / Num. obs: 25039 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Net I/σ(I): 10.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.317 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2978 / CC1/2: 0.749 / Rpim(I) all: 0.539 / Rrim(I) all: 1.425 / % possible all: 100

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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: 2.6→35.903 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.375 / SU ML: 0.394 / Cross valid method: FREE R-VALUE / ESU R: 0.748 / ESU R Free: 0.359
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2954 1231 4.929 %
Rwork0.2448 23744 -
all0.247 --
obs-24975 99.816 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 81.29 Å2
Baniso -1Baniso -2Baniso -3
1-5.221 Å20 Å20 Å2
2---1.351 Å20 Å2
3----3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4937 0 0 43 4980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125041
X-RAY DIFFRACTIONr_angle_refined_deg0.7111.6476827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3535599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77822.047337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40115941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7381555
X-RAY DIFFRACTIONr_chiral_restr0.0630.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023879
X-RAY DIFFRACTIONr_nbd_refined0.1810.22175
X-RAY DIFFRACTIONr_nbtor_refined0.2880.23445
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2107
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0750.26
X-RAY DIFFRACTIONr_mcbond_it2.2737.9862402
X-RAY DIFFRACTIONr_mcangle_it3.87211.9662999
X-RAY DIFFRACTIONr_scbond_it2.5898.2112639
X-RAY DIFFRACTIONr_scangle_it4.33412.1863828
X-RAY DIFFRACTIONr_lrange_it8.015105.0747505
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
2.6-2.6670.396880.38217150.38218030.410.5031000.366
2.667-2.740.3931140.37816260.37917400.540.571000.358
2.74-2.8190.421060.36616430.3717490.6520.6491000.342
2.819-2.9050.355810.3415620.34116430.6830.7181000.308
2.905-30.348820.34215570.34216400.7570.7699.9390.308
3-3.1040.331690.31814780.31915470.7880.7961000.285
3.104-3.220.318540.31614790.31615330.820.7931000.288
3.22-3.3510.346640.28913700.29114350.8310.86399.93030.261
3.351-3.4980.331810.26513490.26814300.8460.8921000.239
3.498-3.6670.278550.24912750.2513300.8840.911000.23
3.667-3.8640.328620.24112470.24513090.8640.9041000.227
3.864-4.0950.272620.23211470.23412120.9020.91999.75250.223
4.095-4.3740.28580.21910740.22211400.9140.92999.29820.212
4.374-4.7180.291430.19610550.19911090.9160.94799.00810.195
4.718-5.160.332580.2259360.2319960.9010.92599.79920.224
5.16-5.7540.371410.2578680.2639090.890.9061000.247
5.754-6.6160.343320.2587880.2618200.8820.9271000.259
6.616-8.0350.235290.2016780.2027070.9330.9441000.21
8.035-11.0890.158310.1235510.1265820.9760.9791000.14
11.089-35.9030.224210.2113460.2123710.9260.94498.92180.227

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