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- PDB-7u6g: Structure of PQS Response Protein PqsE(E182W,E280A) Variant -

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Basic information

Entry
Database: PDB / ID: 7u6g
TitleStructure of PQS Response Protein PqsE(E182W,E280A) Variant
ComponentsQuinolone signal response protein
KeywordsHYDROLASE / Quorum Sensing / PQS / PqsE / mutant
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / : / Quinolone signal response protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsJeffrey, P.D. / Taylor, I.R. / Bassler, B.L.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM134583 United States
National Science Foundation (NSF, United States)MCB-1713731 United States
CitationJournal: Biochemistry / Year: 2022
Title: The PqsE Active Site as a Target for Small Molecule Antimicrobial Agents against Pseudomonas aeruginosa.
Authors: Taylor, I.R. / Jeffrey, P.D. / Moustafa, D.A. / Goldberg, J.B. / Bassler, B.L.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quinolone signal response protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7433
Polymers34,6321
Non-polymers1122
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.621, 60.621, 145.963
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Quinolone signal response protein


Mass: 34631.633 Da / Num. of mol.: 1 / Mutation: E182W,E280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: pqsE, PA14_51380 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2Z6F6
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 27% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.44→29.96 Å / Num. obs: 12028 / % possible obs: 99.2 % / Redundancy: 9.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.032 / Rrim(I) all: 0.1 / Net I/σ(I): 14.7 / Num. measured all: 116855 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.44-2.517.80.93662007980.6590.34211.889.9
10.93-29.967.60.04612871690.9980.0170.054195.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.17-3644refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7KGX

7kgx


Resolution: 2.45→29.96 Å / SU ML: 0.3258 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.4995
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 539 4.5 %
Rwork0.1728 11452 -
obs0.1759 11991 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.5 Å2
Refinement stepCycle: LAST / Resolution: 2.45→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 2 34 2366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692387
X-RAY DIFFRACTIONf_angle_d0.91143240
X-RAY DIFFRACTIONf_chiral_restr0.0486349
X-RAY DIFFRACTIONf_plane_restr0.0052421
X-RAY DIFFRACTIONf_dihedral_angle_d16.1893877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.690.30121090.22882749X-RAY DIFFRACTION97.21
2.69-3.080.2921430.2182828X-RAY DIFFRACTION100
3.08-3.880.23311440.18862867X-RAY DIFFRACTION100
3.88-29.960.22841430.14853008X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.65028049823-3.33849145869-2.047662271512.705977721323.312182734194.99520992106-0.1859819707960.883684018150.16038572508-0.3281797136880.08083991814220.456127795553-0.351797648757-0.006617688609610.06095171018360.4832672310580.0207753078694-0.066149219340.4291956631480.02232253675070.622007572391-25.6262154045-9.75686352478-27.724534349
28.29823183906-0.836313198703-0.07308893294826.32115160271.029119545855.67286215093-0.289197270142-0.447930178857-0.5833360754420.7108101349470.224564695020.613909438234-0.113930689477-0.4062226832140.03972110840230.5156408939980.1076603372550.1478533652290.4262953192810.07148532676480.507973031458-31.7458404735-10.0397998876-14.5725487188
39.24675239371-2.3042035651.206753138074.446199283-0.5071484970265.49448907773-0.34258793634-1.60348058506-0.4284207920611.407199542350.263689376710.416489367078-0.37280009673-0.1743262643220.007467615045511.058667658430.0114500799640.2161287872530.8520157719970.1525669521040.542416147887-29.2700716702-11.7186309842-2.74437242196
46.62513260671-5.174739077455.518627600527.15530909139-5.078909464374.78712466603-1.06054114842-1.74374069890.8969103145261.712349349870.465015407154-0.33791401376-1.90407379843-1.623209552840.6809309762711.313020899180.1391864193940.07466953579190.805767194279-0.211407887580.697631916981-26.89675689033.28924815361-0.0693847774332
58.62419744738-0.470352040056-2.611101493874.181271060482.9617785886.14968913939-0.512696231879-1.336686934190.04599085765890.785672034393-0.05392588629940.928719986557-0.112003243773-0.9318855894020.2518979446850.9913302987160.2071266277030.09161843079540.8160482194040.06608290020220.570728115177-31.4367972268-7.16217290749-4.08260189518
65.862642766322.814247826093.033202212778.805678991662.036324709499.40275273162-0.04397240942380.236237654309-2.273786802570.789859426757-0.0698725564883-0.1325728496951.874019882020.322462104736-0.1232851004120.7711298495350.1063964993510.1223666193310.4635066241770.2153281250370.903922418554-21.1231512487-24.0188594608-13.7720352122
77.74768847166-0.122627445879-0.9554893419165.651075179750.310200410427.53532561134-0.145553585799-0.58021177490.3188386520231.03027978056-0.0556959369892-0.196315341098-0.2929965659780.3682270776630.1493488643430.4827800885780.0838610354274-0.08676745784660.361665673805-0.03281880282020.47207865349-14.231945326-8.27413237566-15.7921162841
85.642650198810.545276089266-0.009640353672476.520565531936.018266347548.009384441160.10291495861-0.101342421487-0.1458520628670.5634643878980.260332516375-0.664784928070.1289471431510.893791823476-0.3539032468510.5180948912140.07339253715040.0006767965454890.3958880393640.0639002973770.493366128133-10.3997852088-11.5056414523-19.2945391033
96.396870364474.606578316973.063890181194.082853780444.390262265719.01051291158-0.4311225091080.0135809187761-0.01602861612280.2770499257411.43892410078-0.504737591434-1.128731821370.912143237389-0.9056855033690.6896053966080.0391945682054-0.1629935180740.728736729289-0.200796285390.6786190731820.2741215509642.90678689159-16.5348521144
107.60882734892-6.084261133492.547285167377.1810510115-4.924442331796.58152597139-0.295289738132-0.7872195074162.75680889585-0.183887311742-0.3418159214021.34379379494-2.083348747730.360848175860.7913512926371.31653704582-0.0513171052299-0.1962002729650.837574330033-0.2156413107191.36674431031-6.9051440600513.7560293723-13.561364643
113.097094081984.810635448633.720017461379.181416492345.717942559984.477952604150.0963275088911-1.315609346082.063041041560.0449118820962-0.1963750126950.144626144031-0.599955362914-0.8039228833090.2045182265011.18478536504-0.0200317670937-0.00728492692630.945560486746-0.18380330311.07862685354-8.908694272886.21761555984-7.86917608694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 232 )
9X-RAY DIFFRACTION9chain 'A' and (resid 233 through 254 )
10X-RAY DIFFRACTION10chain 'A' and (resid 255 through 269 )
11X-RAY DIFFRACTION11chain 'A' and (resid 270 through 297 )

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