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- PDB-7kgw: Structure of PQS Response Protein PqsE in Complex N-(3-(1H-pyrazo... -

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Basic information

Entry
Database: PDB / ID: 7kgw
TitleStructure of PQS Response Protein PqsE in Complex N-(3-(1H-pyrazol-5-yl)phenyl)-1H-indazole-7-carboxamide
Components2-aminobenzoylacetyl-CoA thioesterase
KeywordsHYDROLASE/Inhibitor / Quorum Sensing / PQS / PqsE / inhibitor / Metal Binding Protein / 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-WDY / 2-aminobenzoylacetyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)35,0484
Polymers34,6331
Non-polymers4153
Water3,045169
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)60.712, 60.712, 146.205
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-WDY / N-[3-(1H-pyrazol-3-yl)phenyl]-1H-indazole-7-carboxamide


Mass: 303.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / 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: 1.99→29.72 Å / Num. obs: 22237 / % possible obs: 99.9 % / Redundancy: 15 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.022 / Rrim(I) all: 0.086 / Net I/σ(I): 20.5 / Num. measured all: 333274
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.874 / Num. measured all: 23983 / Num. unique obs: 1612 / CC1/2: 0.86 / Rpim(I) all: 0.23 / Rrim(I) all: 0.905 / Net I/σ(I) obs: 3.4 / % possible all: 98.8

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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: 1.99→29.72 Å / SU ML: 0.2085 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 1118 5.04 %
Rwork0.1648 21068 -
obs0.1674 22186 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.83 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 25 169 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692502
X-RAY DIFFRACTIONf_angle_d0.82853401
X-RAY DIFFRACTIONf_chiral_restr0.0504364
X-RAY DIFFRACTIONf_plane_restr0.0052470
X-RAY DIFFRACTIONf_dihedral_angle_d14.5261947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.080.27941300.20462583X-RAY DIFFRACTION99.3
2.08-2.190.26951380.19382591X-RAY DIFFRACTION100
2.19-2.330.25621390.17492596X-RAY DIFFRACTION99.96
2.33-2.510.20731100.1722640X-RAY DIFFRACTION100
2.51-2.760.23441330.18552615X-RAY DIFFRACTION99.96
2.76-3.160.24771350.1882620X-RAY DIFFRACTION100
3.16-3.980.2011560.15372646X-RAY DIFFRACTION100
3.98-29.720.18851770.14442777X-RAY DIFFRACTION99.93
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)
15.405232758380.41570736901-0.9037621797574.225589845660.09418569480555.93428238882-0.07744696614140.386703326863-0.281038970550.03425352689070.04391554187540.263300647802-0.100142515533-0.1873151866050.01452872886250.1731425890660.0389548862054-0.01461606654240.175370533086-0.01618263180790.267635080277-28.0771538288-10.6719968639-22.2873684498
24.814410605120.005435182230871.482210519543.854135582950.02854127488543.1545026941-0.0291682271656-0.0969327257683-0.1857726104420.3996102552960.09208220697850.354998348333-0.088075051046-0.369770727572-0.05155143887280.2707342126210.04964060567790.08666726607770.2549506203310.02624057861810.221479722143-32.8126689281-8.85689886249-12.982619833
37.551984017370.06474235835631.911490233793.017196964810.002400746392215.17827504732-0.0224271415186-1.06333957799-0.3987804867140.7570140730240.1006135663460.1760993157450.0837762070525-0.241571339752-0.09011455906550.4971021525350.02171360032190.08309840024760.3520147340340.06985952238110.235930538834-29.4624528041-11.5579125618-2.81530041288
43.564814909240.1773995950071.465796241912.538149959631.145804914461.06299239724-0.577417247785-1.010280410220.9131946425210.9486517048440.177644186546-0.136378467439-1.39696822879-0.7048037457370.2363391103420.7544554322210.177467188535-0.07954596845360.500996571516-0.1808452505130.419118707148-27.14191872753.74690288305-0.327906644483
55.466735661631.50451827152-1.525295739291.860844875790.9071762430674.9326710165-0.373940310737-0.7900590965130.1322994603130.6847720608970.2284489171540.681127993404-0.551090813688-0.7469069555120.1424813784350.5911280341310.109014119553-0.03128768567680.464206963882-0.008078803665070.273779150046-31.6012465758-7.05110322139-4.10683750652
68.307076444014.504819950585.002999101782.657304954532.573808876526.101846518080.170206178963-0.0464307470971-1.323861385640.5193591980730.113018553463-0.1309624197860.8707756302260.0201211652907-0.4660177658190.4377962749090.03714096278520.004906210017830.2138634145960.0196926577470.631100038126-21.0745613105-23.9808321316-13.7820965685
73.94745771466-1.55126058406-0.6625285061151.30612388726-0.4572532477665.29600010347-0.187873265376-0.107688264278-0.4512748252650.4511508381140.02317394327290.1441227198210.2124357450160.08453785794410.1093389286030.2308483572970.0218285941763-0.02806903131580.1492145722160.007720449621470.269073302828-16.4240708932-14.8019813949-14.3096350422
84.054564427671.84638448984-0.4860360454625.039907991550.4617508801886.28294525597-0.145746183497-0.177914780884-0.007029153449740.6269295782140.035872528928-0.285851004063-0.2342879023810.2664854526730.1004487276660.21851190324-0.00501327893678-0.09411702929460.210836449911-0.01873080572040.292212977869-8.73064214226-5.06930128275-15.1811560005
98.2958151914-4.92756085768-2.481059135528.623528207240.8907109851033.234836516270.1596792455970.494941622288-0.0370626644991-0.0956717061258-0.128662328778-0.157562425108-0.06744300791050.10768719769-0.03425171402170.199897951549-0.00367627569939-0.03772323966480.215863351125-0.04182634872870.197571824027-14.8325089728-11.5606608916-24.5422822715
104.312087172455.412439982641.398419983346.42140872772.033087624173.31668173975-0.03486590410870.123143739811-0.004297313183080.4775163289260.299321068212-0.528215593692-0.5791808696130.419167137917-0.2920421491010.415442807456-0.0407118730897-0.1225857891630.357780177864-0.03799960624420.423628310410.4399634011692.81455993567-16.4858307954
119.738972788836.505864888483.222110419375.849559672442.844472899432.77606450666-0.140268611723-0.2112269391761.81940013602-0.0957613071768-0.0921587532730.600827336779-0.646797590487-0.1181212956820.2204287118250.7153620546110.0358665293285-0.1655130152660.361761295298-0.024138708390.735031686607-11.686719180611.5190515596-14.5874205666
129.78023729781-6.77494943568-0.4135450423228.928373813540.8936556572092.048302573120.0960392395029-0.448943296573-0.04287920008690.00774180515081-0.3250766781340.425005220785-0.376823218977-0.02492024855330.2421815985330.640008255005-0.0797804187893-0.09973409554860.4191430098-0.09468054764150.395881837041-8.816344164217.18943558544-6.72679211337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 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 177 )
8X-RAY DIFFRACTION8chain 'A' and (resid 178 through 210 )
9X-RAY DIFFRACTION9chain 'A' and (resid 211 through 232 )
10X-RAY DIFFRACTION10chain 'A' and (resid 233 through 254 )
11X-RAY DIFFRACTION11chain 'A' and (resid 255 through 278 )
12X-RAY DIFFRACTION12chain 'A' and (resid 279 through 297 )

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