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- PDB-7r3f: Monomeric PqsE mutant E187R -

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Basic information

Entry
Database: PDB / ID: 7r3f
TitleMonomeric PqsE mutant E187R
Components2-aminobenzoylacetyl-CoA thioesterase
KeywordsHYDROLASE / QUORUM SENSING / PSEUDOMONAS / PROTEIN / PQS / THIOESTERASE
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
BENZOIC ACID / CACODYLATE ION / : / 2-aminobenzoylacetyl-CoA thioesterase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsBorgert, S.R. / Schmelz, S. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa.
Authors: Borgert, S.R. / Henke, S. / Witzgall, F. / Schmelz, S. / Zur Lage, S. / Hotop, S.K. / Stephen, S. / Lubken, D. / Kruger, J. / Gomez, N.O. / van Ham, M. / Jansch, L. / Kalesse, M. / Pich, A. ...Authors: Borgert, S.R. / Henke, S. / Witzgall, F. / Schmelz, S. / Zur Lage, S. / Hotop, S.K. / Stephen, S. / Lubken, D. / Kruger, J. / Gomez, N.O. / van Ham, M. / Jansch, L. / Kalesse, M. / Pich, A. / Bronstrup, M. / Haussler, S. / Blankenfeldt, W.
History
DepositionFeb 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,9445
Polymers34,5741
Non-polymers3714
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.535, 60.174, 128.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein 2-aminobenzoylacetyl-CoA thioesterase


Mass: 34573.574 Da / Num. of mol.: 1 / Mutation: E187R
Source method: isolated from a genetically manipulated source
Details: Mutation at position 187: E187R / Source: (gene. exp.) Pseudomonas aeruginosa 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-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.59 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.16 M CaAcetate, 0.08 M NaCacodylate pH 6.5, 14.4% PEG 8000, 20% Glycerol protein conc: 7.5mg/ml cryoprotectant: 10 % (v/v) (2R,3R) -(-)-2,3-Butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.6→29.29 Å / Num. obs: 88338 / % possible obs: 99.45 % / Redundancy: 8.08 % / Biso Wilson estimate: 12.74 Å2 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.0384 / Net I/σ(I): 14.36
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 8841 / Rpim(I) all: 0.3157 / % possible all: 95.72

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å29.29 Å
Translation1.8 Å29.29 Å

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HIO

5hio


Resolution: 1.65→29.29 Å / SU ML: 0.197 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2386 2115 4.89 %
Rwork0.2038 41116 -
obs0.2055 43231 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 16 266 2599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422413
X-RAY DIFFRACTIONf_angle_d0.74343286
X-RAY DIFFRACTIONf_chiral_restr0.0427358
X-RAY DIFFRACTIONf_plane_restr0.0068429
X-RAY DIFFRACTIONf_dihedral_angle_d5.5415337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.28151500.26112683X-RAY DIFFRACTION99.89
1.69-1.730.30491170.25642706X-RAY DIFFRACTION100
1.73-1.780.26871450.25722693X-RAY DIFFRACTION99.93
1.78-1.830.29731740.25552684X-RAY DIFFRACTION100
1.83-1.890.28091220.25852753X-RAY DIFFRACTION99.97
1.89-1.960.26221250.23872691X-RAY DIFFRACTION100
1.96-2.030.25831210.22562725X-RAY DIFFRACTION100
2.03-2.130.26231250.22062741X-RAY DIFFRACTION100
2.13-2.240.26221610.21422706X-RAY DIFFRACTION100
2.24-2.380.23331460.20712743X-RAY DIFFRACTION100
2.38-2.560.22491280.2012747X-RAY DIFFRACTION99.97
2.56-2.820.2441520.1962752X-RAY DIFFRACTION100
2.82-3.230.21491530.18352766X-RAY DIFFRACTION99.93
3.23-4.070.22491530.16122779X-RAY DIFFRACTION99.46
4.07-29.290.18551430.17552947X-RAY DIFFRACTION99.65
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)
10.2764094687490.0366350807528-0.04292720985160.531551209661-0.132803513350.361997284092-0.0260560394727-0.179510235039-0.10529457190.07178462187370.07586600913320.293492360562-0.00238716552082-0.1754897213280.01106052347480.04310222962660.01644468520620.03386966392580.1060077111770.03290879782590.0872070004753-13.3271122865-12.989000298827.7146946759
20.1819755351620.0712340769445-0.06670088250170.0651868589230.04086000864560.113122438935-0.0149881070636-0.0226445856811-0.013313279699-0.02273917406250.02562383855950.006186777678-0.06577016225130.103072914028-0.002519165379360.0771887100741-0.00234877110748-0.001795541743070.0484903680239-0.01635398675610.06336258880651.16666201295-6.0916669018519.7941772621
30.02526316127040.0212623335512-0.02831751897760.02677614773170.02424949339290.0791767679585-0.02265632733910.07119818828340.0452273716503-0.07427724790810.002982431474650.0122783682977-0.09107405475630.203949912375-0.0009290122372970.106121895699-0.0205188439950.02101410928390.14396304092-0.03816443614340.07813067814637.2255362899-8.168933037763.57983118134
40.2873240760780.1279783951070.02113313802570.08782502838380.01726091007950.0117409634046-0.03640817269490.148478071896-0.215717443259-0.0479759932570.0445725873285-0.0994146124640.0211431488717-0.0569108216874-0.005585462003220.115986707135-0.004917761281490.00553201597630.106149244626-0.04781889038980.0911164797797-1.94087741375-19.78256571124.78231201435
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 185 )18 - 1851 - 168
22chain 'A' and (resid 186 through 249 )186 - 249169 - 232
33chain 'A' and (resid 250 through 271 )250 - 271233 - 254
44chain 'A' and (resid 272 through 311 )272 - 311255 - 294

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