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- PDB-7r3e: Fusion construct of PqsE and RhlR in complex with the synthetic a... -

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Basic information

Entry
Database: PDB / ID: 7r3e
TitleFusion construct of PqsE and RhlR in complex with the synthetic antagonist mBTL
Components2-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 / transcription cis-regulatory region binding / hydrolase activity / 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 / 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 / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Beta-Lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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: 3.46 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,Regulatory protein RhlR
B: 2-aminobenzoylacetyl-CoA thioesterase,Regulatory protein RhlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6208
Polymers131,6802
Non-polymers9406
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-77 kcal/mol
Surface area44300 Å2
Unit cell
Length a, b, c (Å)159.651, 159.651, 288.743
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 70 or resid 72...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLYSA4 - 73
d_12ens_1TYRASPA75 - 304
d_13ens_1GLYILEA309 - 545
d_14ens_1FEFEB
d_15ens_1FEFEC
d_16ens_1K5GK5GE
d_21ens_1METLYSF1 - 70
d_22ens_1TYRILEF72 - 538
d_23ens_1FEFEG
d_24ens_1FEFEH
d_25ens_1K5GK5GJ

NCS oper: (Code: givenMatrix: (-0.958137545896, -0.122024580136, 0.259002789535), (-0.236562541907, -0.172172960344, -0.956239842034), (0.161278042245, -0.977479653788, 0.136098932842)Vector: -57. ...NCS oper: (Code: given
Matrix: (-0.958137545896, -0.122024580136, 0.259002789535), (-0.236562541907, -0.172172960344, -0.956239842034), (0.161278042245, -0.977479653788, 0.136098932842)
Vector: -57.1148392797, -92.3608277728, -70.8983872578)

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Components

#1: Protein 2-aminobenzoylacetyl-CoA thioesterase,Regulatory protein RhlR / Elastase modulator


Mass: 65839.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PqsE-XTEN30-RhlR fusion construct,PqsE-XTEN30-RhlR fusion construct
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, rhlR, lasM, vsmR, PA3477 / Production host: Escherichia coli (E. coli)
References: UniProt: P20581, UniProt: P54292, 2-aminobenzoylacetyl-CoA thioesterase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaAcetat pH 4.22 1.029 M (NH4)2HPO4 Cryo: 10% (v/v) 2,3-Butandiol protein concentration: 12 mg/ ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.46→144.372 Å / Num. obs: 19574 / % possible obs: 94.8 % / Redundancy: 26.8 % / Biso Wilson estimate: 155.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.5
Reflection shellResolution: 3.46→3.7 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 980 / CC1/2: 0.562

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC1.0.5 (20210420)data reduction
autoPROC1.0.5 (20210420)data scaling
autoPROC1.0.5 (20210420)data processing
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HIQ

5hiq


Resolution: 3.46→53.54 Å / SU ML: 0.4467 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.3229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 943 4.82 %
Rwork0.2284 18611 -
obs0.229 19554 78.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 175.01 Å2
Refinement stepCycle: LAST / Resolution: 3.46→53.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8603 0 44 3 8650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318856
X-RAY DIFFRACTIONf_angle_d0.674912028
X-RAY DIFFRACTIONf_chiral_restr0.04171308
X-RAY DIFFRACTIONf_plane_restr0.00591576
X-RAY DIFFRACTIONf_dihedral_angle_d15.73753272
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 5.64583802085 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.46-3.640.4054200.3625549X-RAY DIFFRACTION16.4
3.64-3.870.3557850.35551753X-RAY DIFFRACTION53.31
3.87-4.170.36271350.31482721X-RAY DIFFRACTION81.58
4.17-4.590.32781830.28023300X-RAY DIFFRACTION99.26
4.59-5.250.25371590.24613363X-RAY DIFFRACTION100
5.25-6.620.27391810.263376X-RAY DIFFRACTION100
6.62-53.540.18351800.17563549X-RAY DIFFRACTION99.71
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)
14.65170399523-0.449499944451-0.5107471825147.05917371559-0.4957700466254.41116359762-0.396913571738-0.378781047034-0.3877510040010.88237985353-0.254063376322-0.977080252875-0.1599672610360.8412363130830.4581689655831.06281987724-0.0154966945424-0.2456173241751.345513280830.2033478945121.509809340675.03254598944-66.9173669616-24.924418225
20.837771896579-0.261256342276-0.7492050521122.68716673163-3.094103690844.913580793510.895241699739-1.04040611242-0.4074935347891.59993852997-0.4269744743190.00886485651493-0.585488711534-0.4393886551720.7746321904612.26868570282-0.243742286225-0.6917507696511.98559612587-0.1027348405321.541322157995.58075993738-51.7239911072-14.8601015062
35.44268545461-1.80674901924-0.2711833451047.65124947023-3.205068273482.29833993767-0.289065827154-0.0232304527620.7154232083760.580188246928-0.465619914872-1.34271109462-0.5135240060080.7062599630610.5153202427031.27140392866-0.177141497677-0.2812246599011.218578200190.1042092560721.581416224893.19340800661-55.6432711508-26.4236970782
46.24495220035-3.16500358188-2.059677224028.357419338722.198573021893.00849429632-0.306535582864-0.510331752228-0.2167642293151.1628074551-0.2343270161810.389306247741-0.37266236481-0.2020420090090.1311446260941.407325090280.0948699715564-0.03636800373361.1678736174-0.07286585788520.939216765808-16.9065300567-58.3175861527-20.8642758017
51.92107724284-1.70633391737-0.09286466240184.829787211912.020970141661.66783588376-0.879504988925-0.821728310974-0.8004400429121.078876828641.43497518221-0.0753592033083-0.229115003668-0.03522581300970.475090313491.967618924590.204904757331-0.01657920426131.79280066969-0.1065627370731.04031750433-19.809424205-43.9874171482-19.3677836084
65.38211178332-1.85491153093-1.03356627451.182699013140.5454532897912.21145943551-0.0145950813590.4617521294890.462513509542-0.8505391336790.1803021802-0.205083616217-0.4650995836110.3146513947140.2282400761811.412912620.130828721112-0.2245190709461.49596817595-0.3054136455181.04460317829-18.3733232878-34.5271560837-52.3018835534
75.19159172277-2.016075512240.132618717395.74163239572-1.456293648753.249919846580.147052719663-0.315726183599-0.834644007512-0.343784658175-0.004334229909350.9357375718980.0828268916496-0.2224133811240.2068761262491.22072891060.0250076133546-0.03671753842881.48663033722-0.02912365388220.978872692076-21.9820445232-40.307970766-49.5403291347
82.4723053903-0.02720088050891.636456314476.33344812294-0.8639603125631.20045831902-0.0896811851643-0.2016847223140.479203791389-0.515554683289-0.2293307330680.106268471862-0.5409184103540.3262897698750.08290092263021.6524172394-0.0554721886087-0.1449184720031.542446755860.03420042566151.12681824798-36.7863122234-9.02546797234-60.114926165
91.45563191005-0.85996429691-0.2623469743960.5593930081730.2541931004340.323476648687-0.612880269258-1.23496349169-1.13579906781.523757610410.8214655325582.03037350552-0.0567507888409-0.5340496331220.0009460297150331.657352551390.8675722412131.278797193051.78511493750.6922419242532.9710865723-59.0835796118-55.5388223578-12.1663618803
101.84835411822-1.00595009713-1.216457295243.056007124280.7530526020130.790474277752-0.63609834549-0.334487400684-1.308189444470.9489850478630.114117067562.369382609571.15280398586-0.734239861295-0.9094417855682.036167892490.1366730949170.9441867194261.992701173180.9558260097993.40733589937-59.1632334738-71.8965652944-20.1564517142
111.150553351531.528343686190.8368723918293.02704131179-0.1059625734751.93439577535-0.2892904413090.25094495632-0.3127521684630.4609691510950.9329415273842.57006469139-0.186137043404-1.03980652319-0.534724124080.9612048218420.4553019181720.5806388260911.453210846490.5855679251892.39528972438-57.9024944794-59.4443870847-23.2781200211
122.57999149837-0.140291068422-0.3708836096337.198437270530.3246182435951.36220584909-0.00562202742416-0.113401018598-0.7619665675561.365670576580.4646390619440.941830860407-0.184817537069-0.111522745517-0.2167131295621.366400877910.4095756600250.3934036276121.332689071990.09521764976051.53068136921-37.1025514232-61.5477295803-20.585758559
133.09274852711-3.470684325260.3855942373093.93764267319-0.04604173511751.56452560848-0.452868799805-0.217635731154-0.1335364291280.09068251662660.2208530458621.25009196906-0.1901114146790.0932561653991-0.3338154600161.19671001533-0.0283372134345-0.04059408191591.1599481251-0.1004106663071.93004860678-38.8711827252-64.1263566001-29.83664816
141.7106080678-0.3302389764961.078358625787.1512907739-1.924217206594.65200256366-0.216857080371-0.26590311604-0.315358782756-0.3424793424680.21926757711.694327550540.120761686402-0.770776087265-0.2920517294821.041369373430.151101849022-0.1666823197661.336046335320.1397017248121.8050807003-51.6473567399-30.3118516146-45.584260168
153.43060146238-0.1469393329820.5916536995287.8870552566-0.6422975528752.18011715336-0.147927238658-0.238959240614-0.5213066202580.08144074392750.320734565830.597280833368-0.09304016526560.0395134266204-0.1904170117010.9549333623880.0732644782621-0.02582254312451.106450585010.02930300823841.27934300401-47.0362663223-31.0638283818-39.366281857
160.9883181921431.65816513107-1.291265530523.54467259152-2.661918698181.99371481998-0.495589146994-0.0338909215713-1.88371909076-1.319730781620.1206879419560.1898614405811.44835755404-0.822394941463-0.1061905786831.685574928350.056150865846-0.419453156361.77925427064-0.4118321554261.4466301476-38.7651448227-30.7320219146-68.8676820333
171.001568970740.3959031801350.9799228861312.708990249570.4231871849810.9472111300750.09595368202042.18084549513-0.663799975867-1.2683882421-0.0315342543764-0.2274167173260.620084098869-0.1585359002420.1252425026532.494418459510.115006687308-0.3336468160712.17602106889-0.1539475996061.23243883975-35.4578747993-20.5571783209-76.2890773021
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 88 )AA-2 - 881 - 91
22chain 'A' and (resid 89 through 116 )AA89 - 11692 - 119
33chain 'A' and (resid 117 through 168 )AA117 - 168120 - 171
44chain 'A' and (resid 169 through 273 )AA169 - 273172 - 276
55chain 'A' and (resid 274 through 354 )AA274 - 354277 - 327
66chain 'A' and (resid 355 through 429 )AA355 - 429328 - 402
77chain 'A' and (resid 430 through 500 )AA430 - 500403 - 473
88chain 'A' and (resid 501 through 572 )AA501 - 572474 - 545
99chain 'B' and (resid 1 through 88 )BF1 - 881 - 88
1010chain 'B' and (resid 89 through 116 )BF89 - 11689 - 116
1111chain 'B' and (resid 117 through 168 )BF117 - 168117 - 168
1212chain 'B' and (resid 169 through 273 )BF169 - 273169 - 273
1313chain 'B' and (resid 274 through 354 )BF274 - 354274 - 320
1414chain 'B' and (resid 355 through 428 )BF355 - 428321 - 394
1515chain 'B' and (resid 429 through 499 )BF429 - 499395 - 465
1616chain 'B' and (resid 500 through 524 )BF500 - 524466 - 490
1717chain 'B' and (resid 525 through 572 )BF525 - 572491 - 538

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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