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- PDB-7r3j: Nativ complex of PqsE and RhlR with the synthetic antagonist mBTL -

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Basic information

Entry
Database: PDB / ID: 7r3j
TitleNativ complex of PqsE and RhlR with the synthetic antagonist mBTL
Components
  • 2-aminobenzoylacetyl-CoA thioesterase
  • Regulatory protein RhlR
KeywordsTRANSCRIPTION / QUORUM SENSING / LuxR-type TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / DNA BINDING PROTEIN / GENE REGULATION / mBTL / rhamnolipid / PQS
Function / homology
Function and homology information


positive regulation of pyocyanine biosynthetic process / positive regulation of secondary metabolite biosynthetic process / 2-aminobenzoylacetyl-CoA thioesterase / quorum sensing / secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of proteolysis / positive regulation of lipid biosynthetic process / protein-DNA complex ...positive regulation of pyocyanine biosynthetic process / positive regulation of secondary metabolite biosynthetic process / 2-aminobenzoylacetyl-CoA thioesterase / quorum sensing / secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of proteolysis / positive regulation of lipid biosynthetic process / protein-DNA complex / signaling receptor activity / gene expression / hydrolase activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / metal ion binding / cytoplasm
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / : ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Chem-K5G / 2-aminobenzoylacetyl-CoA thioesterase / HTH-type quorum-sensing regulator RhlR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 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
B: 2-aminobenzoylacetyl-CoA thioesterase
C: Regulatory protein RhlR
D: Regulatory protein RhlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,02010
Polymers128,0804
Non-polymers9406
Water41423
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)159.256, 159.256, 284.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 20 or (resid 21...
d_2ens_1(chain "B" and (resid 1 through 286 or (resid 287...
d_1ens_2(chain "C" and ((resid 3 through 4 and (name N...
d_2ens_2(chain "D" and (resid 3 through 227 or (resid 228...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METASPA4 - 304
d_12ens_1FEFEB
d_21ens_1METASPE1 - 301
d_22ens_1FEFEF
d_11ens_2ASNILEI3 - 241
d_12ens_2K5GK5GJ
d_21ens_2ASNILEK1 - 239
d_22ens_2K5GK5GL

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.987872536261, -0.0723181281373, 0.137397017598), (-0.0839366231351, -0.495720375376, -0.864416538906), (0.130623487164, -0.865466000361, 0.483638405031)-55.2150910752, -109.504650267, -58.6708809411
2given(-0.986370503104, -0.0792357490257, 0.144204461385), (-0.131098358173, -0.151154598546, -0.97977829524), (0.0994306345715, -0.985329378134, 0.138706760808)-64.6707174423, -87.9821141405, -69.6001868837

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Components

#1: Protein 2-aminobenzoylacetyl-CoA thioesterase


Mass: 36428.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: Protein Regulatory protein RhlR / Elastase modulator


Mass: 27611.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: rhlR, lasM, vsmR, PA3477 / Production host: Escherichia coli (E. coli) / References: UniProt: P54292
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-K5G / 4-(3-bromophenoxy)-N-[(3S)-2-oxothiolan-3-yl]butanamide


Mass: 358.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16BrNO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaAcetate pH 4.90, 0.970 M (NH4)2HPO4, 10 mM TCEP pH7 equal mixture of His6-PqsE and RhlR (10mg/ml) Cryoprotectant: 20% (w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.06→47.47 Å / Num. obs: 25599 / % possible obs: 95 % / Redundancy: 27.2 % / Biso Wilson estimate: 102.33 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 17
Reflection shellResolution: 3.06→3.326 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1830 / CC1/2: 0.591 / Rpim(I) all: 0.541 / % possible all: 74.8

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
autoPROCdata reduction
STARANISOdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HIQ

5hiq


Resolution: 3.06→47.47 Å / SU ML: 0.507 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.0483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2893 1248 4.88 %
Rwork0.269 24344 -
obs0.27 25592 73.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 112.53 Å2
Refinement stepCycle: LAST / Resolution: 3.06→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8623 0 44 23 8690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288867
X-RAY DIFFRACTIONf_angle_d0.612512041
X-RAY DIFFRACTIONf_chiral_restr0.04061308
X-RAY DIFFRACTIONf_plane_restr0.00491581
X-RAY DIFFRACTIONf_dihedral_angle_d14.26663279
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.10295873795
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.69512143915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.190.5268300.4934461X-RAY DIFFRACTION12.92
3.19-3.330.4392660.38541338X-RAY DIFFRACTION37.18
3.33-3.510.35371040.38411819X-RAY DIFFRACTION50.87
3.51-3.730.45451110.37542462X-RAY DIFFRACTION67.55
3.73-4.010.36741750.33893365X-RAY DIFFRACTION92.12
4.01-4.420.33492010.29093641X-RAY DIFFRACTION100
4.42-5.060.30751610.25843676X-RAY DIFFRACTION100
5.06-6.370.26922040.27183699X-RAY DIFFRACTION99.92
6.37-47.470.21471960.20673883X-RAY DIFFRACTION99.85
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)
14.265626671911.50592795919-0.7535477766631.90778271414-0.04853835463351.40422039161-0.359037763955-0.307747550037-0.925953168260.743338178243-0.464949145609-0.739862953726-0.4399356366490.4124172851090.5489460183010.700297771285-0.0884132742061-0.5059222689020.5329328879580.1739815881491.265255275515.0693758378-64.7480745847-24.6785888741
22.651885013410.1221647058070.3841338531881.71440865909-1.607485997651.58966489103-0.0885555413474-1.161445472110.06363668874261.25212543009-0.0301509654441-0.806368236521-0.2662239039960.0531224467874-0.04228598482661.57697676136-0.194240451273-0.8995838449061.1620996034-0.02193191189831.212825640698.74175770848-57.0591251679-11.7541094442
35.39461338485-0.417833932195-0.7514454173923.98441715568-0.106891356212.17902464416-0.01915682844020.1505594167050.07099919759330.804939365733-0.1858503139970.013482709194-0.732052923035-0.01990656143870.1126286757910.7754222638130.0401972469701-0.2032120674940.28791313287-0.04273982283310.380474598431-12.2683942662-56.8858679761-26.5897889022
40.49818966716-0.3705356083660.08470518637151.27213302846-0.5854771613660.286938921803-0.116361759462-0.486539016708-0.2043443534090.8797177296760.1087181193910.0049842348294-0.1315394155140.186259798413-0.1844923238792.331395418730.4565972292130.0407921462050.7985788461120.1069202834950.651746977354-17.4892575434-54.9321282156-8.04668296552
50.807317760937-0.4114953189540.03671336123311.0905046140.3931609851390.190642990421-0.168423538953-0.383114455041-0.4390946094920.7301644893250.4475408019510.94152313874-0.241318654483-0.2163051682630.125420683841.945042789110.8625878738461.13209959451.22827193830.5693861753442.04122607623-56.7152139891-52.79657215-9.97707612538
60.870666477521-0.4284271084180.1073813022490.273496099954-0.176198882550.216426429604-0.0675243345046-0.109807700602-0.6715639178870.6852073448620.4003627224171.18866497537-0.229994436535-0.6529940889850.4613600470271.318462936020.4259672839041.06910234251.093274877880.6984739530752.99256651378-61.2876169068-62.6464696889-19.2222700348
71.75024598689-0.9436685424440.1319202027231.659444780870.1492802280940.8168858381050.0577869963584-0.00504977818305-0.5986627091930.9198592096970.4689185989621.15728726046-0.252361097419-0.248305726984-0.3677787079091.047478601920.5356469990860.7845219161740.5004458721910.245466944221.74770179592-38.1918578178-63.5632047442-20.9955513637
81.96090361595-0.40712454924-1.061588262322.9169785188-0.3106685282330.9499654037960.07113490406590.469721996585-0.273033868524-0.1016968175420.08684311940290.495841739781-0.3638775620150.1827242729610.1603552649720.8441583941540.0774795055935-0.3145219760960.94203152752-0.2841543267210.112512506773-20.9381229409-36.6065297662-47.7524981243
95.80435172307-5.582445632681.957544641579.72957464634-4.293711096181.991220261640.2426275140010.688013700582-0.0994766485779-1.03173077393-1.06298587874-0.551122094978-0.0900845046208-0.5961391506240.4017495196321.39047733229-0.300328672165-0.185813161081.0233685386-0.2241958146970.69819798464-25.6017318842-15.5673802626-49.6150479916
101.450225208850.665185051828-0.410787790383.030798177890.859885534431.20286959215-0.0477027184019-0.02886636161680.356109800554-0.324275820103-0.03818107910440.520503245822-0.3922689940140.1898287662080.1858918887371.22606141670.021897990561-0.5071935887970.902845668432-0.04478845368530.398722353626-39.0606677838-6.96901393523-61.5552486036
113.29592152026-1.978487562570.4999854697261.6515136159-0.7587805050150.527525446431-0.01500099353980.148024336073-1.24507005484-0.2068047814130.3247856704591.573871105930.32055975186-0.226685090315-0.2591591152030.6504895703370.275182368235-0.2809102608410.795407491092-0.1799153102581.66537294521-38.1323366814-49.4069550923-40.4271792233
122.40861880865-0.008812007155230.3372725453881.58590937461-0.3487995799181.93946454074-0.4576577638050.302473895677-0.463117391529-0.01003826416840.6444903433841.94114466762-0.0434185893915-0.41239182471-0.2746388258590.5788690131780.152533979557-0.07275793811640.8373441208670.2313242640811.52891766829-51.3260562572-30.9864061944-45.4846826856
134.74521297451-2.19921402594-0.1185137788714.90485118790.1692749146712.02240272485-0.522261096412-0.0978299176185-0.4372011957620.6449566673860.4958973404331.14138177121-0.0164415477205-0.1464497390630.01724705169460.597133897530.1786073749120.02212582965650.5213491132690.2522578260120.987219017748-46.9584820357-30.8264486676-38.8120605232
140.433482805894-0.102668633147-0.02058600645370.146889294926-0.184742775070.2738092988270.08142250389790.0496555214539-0.762584360185-0.814158040329-0.1331334779010.5807551950910.596911656578-0.707435169316-0.2813835878911.37325846716-0.0725618221135-0.6017598302481.32079761516-0.4684242650461.24246871652-38.55669411-30.0673073678-68.2417172591
151.992644494771.08029531494-0.01805834686061.58972768690.6411653251670.473488673760.003502757444741.31927215138-0.55113708037-1.185174439750.3660487162790.07426647314650.332609857036-0.103828028797-0.06927393076331.59494500742-0.052863593925-0.4922936486651.41344139934-0.3171738054210.555430696552-35.1155031843-19.8381940825-75.5220565642
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 101 )AA-2 - 1011 - 104
22chain 'A' and (resid 102 through 137 )AA102 - 137105 - 140
33chain 'A' and (resid 138 through 253 )AA138 - 253141 - 256
44chain 'A' and (resid 254 through 301 )AA254 - 301257 - 304
55chain 'B' and (resid 1 through 54 )BE1 - 541 - 54
66chain 'B' and (resid 55 through 155 )BE55 - 15555 - 155
77chain 'B' and (resid 156 through 301 )BE156 - 301156 - 301
88chain 'C' and (resid 1 through 169 )CI1 - 1691 - 169
99chain 'C' and (resid 170 through 182 )CI170 - 182170 - 182
1010chain 'C' and (resid 183 through 241 )CI183 - 241183 - 241
1111chain 'D' and (resid 3 through 19 )DK3 - 191 - 17
1212chain 'D' and (resid 20 through 97 )DK20 - 9718 - 95
1313chain 'D' and (resid 98 through 168 )DK98 - 16896 - 166
1414chain 'D' and (resid 169 through 193 )DK169 - 193167 - 191
1515chain 'D' and (resid 194 through 241 )DK194 - 241192 - 239

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