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- PDB-7kgx: Structure of PQS Response Protein PqsE in Complex with 4-(3-(2-me... -

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Basic information

Entry
Database: PDB / ID: 7kgx
TitleStructure of PQS Response Protein PqsE in Complex with 4-(3-(2-methyl-2-morpholinobutyl)ureido)-N-(thiazol-2-yl)benzamide
Components2-aminobenzoylacetyl-CoA thioesterase
KeywordsHYDROLASE/Inhibitor / Quorum Sensing / PQS / PqsE / inhibitor / HYDROLASE-Inhibitor complex
Function / homology
Function and homology information


2-aminobenzoylacetyl-CoA thioesterase / secondary metabolite biosynthetic process / hydrolase activity / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Chem-WE1 / 2-aminobenzoylacetyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJeffrey, P.D. / Taylor, I.R. / Bassler, B.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM134583 United States
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)MCB-1713731 United States
Alexander von Humboldt Foundation United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Inhibitor Mimetic Mutations in the Pseudomonas aeruginosa PqsE Enzyme Reveal a Protein-Protein Interaction with the Quorum-Sensing Receptor RhlR That Is Vital for Virulence Factor Production.
Authors: Taylor, I.R. / Paczkowski, J.E. / Jeffrey, P.D. / Henke, B.R. / Smith, C.D. / Bassler, B.L.
History
DepositionOct 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-aminobenzoylacetyl-CoA thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1624
Polymers34,6331
Non-polymers5293
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.885, 60.885, 146.601
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 2-aminobenzoylacetyl-CoA thioesterase


Mass: 34632.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pqsE, PA1000 / Production host: Escherichia coli (E. coli)
References: UniProt: P20581, 2-aminobenzoylacetyl-CoA thioesterase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-WE1 / 4-({[(2R)-2-methyl-2-(morpholin-4-yl)butyl]carbamoyl}amino)-N-(1,3-thiazol-2-yl)benzamide


Mass: 417.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M MgCl2, 32% (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: 0.9198 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2→29.81 Å / Num. obs: 21904 / % possible obs: 99.7 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.031 / Rrim(I) all: 0.119 / Net I/σ(I): 15.5 / Num. measured all: 324985 / Scaling rejects: 4
Reflection shellResolution: 2→2.06 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.456 / Num. measured all: 18718 / Num. unique obs: 1541 / CC1/2: 0.71 / Rpim(I) all: 0.424 / Rrim(I) all: 1.518 / Net I/σ(I) obs: 1.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.17-3644refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q0I

2q0i


Resolution: 2→29.81 Å / SU ML: 0.2274 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 1027 4.7 %
Rwork0.1745 20827 -
obs0.1766 21854 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.68 Å2
Refinement stepCycle: LAST / Resolution: 2→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 31 102 2533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672508
X-RAY DIFFRACTIONf_angle_d0.84263406
X-RAY DIFFRACTIONf_chiral_restr0.0498368
X-RAY DIFFRACTIONf_plane_restr0.0053456
X-RAY DIFFRACTIONf_dihedral_angle_d14.5679951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.28611600.25072890X-RAY DIFFRACTION98.64
2.11-2.240.22711230.21372942X-RAY DIFFRACTION100
2.24-2.420.22531530.18852909X-RAY DIFFRACTION99.97
2.42-2.660.22981260.18992981X-RAY DIFFRACTION100
2.66-3.040.23521600.19332952X-RAY DIFFRACTION100
3.04-3.830.21191610.17292997X-RAY DIFFRACTION100
3.83-29.810.20921440.14953156X-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)
14.1877234582-0.878416731138-3.785387430884.028733086140.5749992044813.892976482890.1684135048680.9915397147610.00893157083049-0.4172911495010.1488425967640.0743537144876-0.293455939289-0.126881715661-0.4373600547470.284286029860.000432286527218-0.04883526662890.399166371333-0.02310429578060.371691754758-25.4804138295-9.36939817178-28.1371299018
25.841642005450.09340212851220.7778753806123.38040296967-0.2098008420254.08593477579-0.0889734735137-0.19347360486-0.4041551752760.3480293905450.08654343459540.321550386781-0.0389548064348-0.463078661830.01306926166120.2714611427370.05105535176690.08427690291610.2501314091820.02363222844120.294834588062-31.9215112845-9.85222036288-14.7928527217
37.40670930866-0.4168359967952.312338181022.738607294080.6579113108044.0219321827-0.100455034944-1.41540079565-0.4470437078320.9239357347820.134226683450.2836976290330.120999664014-0.33528288597-0.04268614825840.6373637886630.04174183828570.08553961441750.5079823050480.1329552381170.33009942749-29.0806490704-11.5102916666-2.70651609899
43.01420794683-2.146577991332.702344768721.53495280052-1.945410072962.56680145665-0.823347124779-1.168613856760.8179632493121.509445759850.321193903169-0.293729778984-1.57822417739-1.155365835270.3098210586371.012326447510.181364730786-0.03861271185920.666482704405-0.1876428839970.467777696957-27.46452686073.47762884509-0.317553471266
55.97425444412-0.5443099420170.01425234540411.935969207970.8924494588634.31024155513-0.297877850666-0.536368921725-0.3875988618030.4893647165010.1845432782990.192159451974-0.0308320010992-0.3804908157260.1319836707310.5002346688610.03005524101460.05498838584050.3235757280810.1401934882050.326604027183-27.5535298914-13.7505065155-8.03403226417
63.8101681593-0.5244215334570.0477039959452.788066452330.131397360314.27552504328-0.101079319197-0.2141838238720.01232240579890.549237418628-0.0477106884665-0.12263845152-0.1730759798910.1499955135840.1332128437030.2384878801520.029475052444-0.06598424287730.190312864371-0.01189385844190.26659369075-14.3185567621-8.26488875486-15.8285876588
74.105568882340.145183838385-0.09081889437125.927574957422.855322853336.85878751608-0.01975913869510.161154032996-0.3232605254330.297996074990.0845974007549-0.4448920480250.1581693796410.585440982169-0.05449800602350.199653055230.00957995589613-0.02325165230680.1679054378070.02740052707610.25890530239-10.5019257442-11.4566649308-19.3088786167
89.134908531127.911227925010.2005295408968.472852574841.421123411183.5388236615-0.1021427997250.0245716538920.2579617206760.3860766121410.356537689281-0.218693114934-0.8203355642020.687126351813-0.2686819837590.434956710357-0.0445975741625-0.1539329022360.397517534043-0.04018524755060.400353960020.4498510221412.8693822991-16.5496854464
95.59817183914.893706270233.684556946424.674801310232.661377041814.02079212229-0.574758346567-0.2431056133052.36771382091-0.2444551165540.04609345604120.589255898147-1.0862523443-0.103878385240.5107046626350.881510812140.0090073698582-0.2362586130530.428481335312-0.01720738750260.861170579771-11.813359644311.4708487135-14.2972315543
107.90894485319-5.75945572031-3.029975153167.811078785561.02847810488.71193203133-0.03189679039-0.7681618762130.319416934762-0.0534565949642-0.1143793086240.449183499785-0.7071502500260.3322472021730.1955190571250.736861768339-0.133431952555-0.1229280526110.446646026371-0.1320256671630.486166350431-7.978881614816.8852247285-6.65134011375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 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 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 197 )
7X-RAY DIFFRACTION7chain 'A' and (resid 198 through 232 )
8X-RAY DIFFRACTION8chain 'A' and (resid 233 through 254 )
9X-RAY DIFFRACTION9chain 'A' and (resid 255 through 278 )
10X-RAY DIFFRACTION10chain 'A' and (resid 279 through 298 )

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