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- PDB-7r3g: PROSS optimitzed variant of RhlR (75 mutations) in complex with t... -

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Basic information

Entry
Database: PDB / ID: 7r3g
TitlePROSS optimitzed variant of RhlR (75 mutations) in complex with the synthetic antagonist mBTL
ComponentsRegulatory protein RhlR
KeywordsTRANSCRIPTION / QUORUM SENSING / LuxR-type TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / DNA BINDING PROTEIN / GENE REGULATION / mBTL / rhamnolipid
Function / homology
Function and homology information


positive regulation of pyocyanine biosynthetic process / positive regulation of secondary metabolite biosynthetic process / quorum sensing / 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 ...positive regulation of pyocyanine biosynthetic process / positive regulation of secondary metabolite biosynthetic process / quorum sensing / 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 / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-K5G / HTH-type quorum-sensing regulator RhlR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHenke, S. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)281361126/GRK2223 Germany
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Regulatory protein RhlR
A: Regulatory protein RhlR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3124
Polymers55,5952
Non-polymers7172
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-22 kcal/mol
Surface area20450 Å2
Unit cell
Length a, b, c (Å)164.780, 164.780, 40.311
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Regulatory protein RhlR / Elastase modulator


Mass: 27797.574 Da / Num. of mol.: 2
Mutation: L9D: D12E: G13D: P20S: H22T: G26E: G46C: T50P: K57R: T58I: E59F: V60M: H61F: T63N: K66P: L69Q: R71H: M74A: G78F: V80I: A83T: L85R: N86H: G87C: S91G: E92N: M93H: V94I: S99D: D102A: Q103D: ...Mutation: L9D: D12E: G13D: P20S: H22T: G26E: G46C: T50P: K57R: T58I: E59F: V60M: H61F: T63N: K66P: L69Q: R71H: M74A: G78F: V80I: A83T: L85R: N86H: G87C: S91G: E92N: M93H: V94I: S99D: D102A: Q103D: S104A: R105Q: M106E: N109D: E110D: W114Y: C117R: V118H: L122H: P123S: I124C: R125M: N129G: L130V: L131M: S132G: V133F: D139S: Q140S: Q141P: N142A: S145P: F146H: I151L: L155M: M158L: T163H: K165T: D168E: E170N: M173S: M175Q: S176P: N177Q: V179I: H183K: Q190R: S197T: G199A: I203K: S206G: H216L: D224N: L230Q
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
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M NaCl, 25 % (w/v) PEG 3350 3.5 mg/ml protein 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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→47.57 Å / Num. obs: 34628 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 35.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.053 / Rrim(I) all: 0.238 / Net I/σ(I): 11.1 / Num. measured all: 697687 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.2219.82.3045855429610.6590.5292.3651.6100
8.86-47.5717.40.06996315530.9970.0170.07136.699.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure prediction of phyre2

Resolution: 2.15→47.57 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 1739 5.03 %
Rwork0.1994 32864 -
obs0.2009 34603 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.8 Å2 / Biso mean: 51.2426 Å2 / Biso min: 21.46 Å2
Refinement stepCycle: final / Resolution: 2.15→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 72 136 3945
Biso mean--34.68 44.32 -
Num. residues----472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.210.30681560.263626912847
2.21-2.280.26881240.248527122836
2.28-2.370.2791700.251527152885
2.37-2.460.26261370.225527102847
2.46-2.570.25961490.227727032852
2.57-2.710.26581420.226327252867
2.71-2.880.28061270.244727522879
2.88-3.10.23731260.212227612887
3.1-3.410.23261610.206927002861
3.41-3.910.22261560.182327372893
3.91-4.920.18381330.153127902923
4.92-47.570.20181580.183928683026
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)
14.7576-1.8821.29436.9907-0.9734.4740.0224-0.6350.97430.6827-0.0341-0.1693-0.6211-0.0621-0.06310.4115-0.03980.14930.3761-0.13150.56827.1663-39.43739.2388
23.85561.10890.89060.73250.66770.60750.1512-0.1074-0.11250.0246-0.0125-0.05660.06690.0313-0.1090.2507-0.01350.02770.32390.0380.206533.8598-57.6090.299
33.57920.64391.40444.94610.7354.4242-0.00850.65650.3576-0.22610.0944-0.3713-0.15530.243-0.06940.1959-0.03860.05880.31010.0340.241132.2477-51.1991-9.0003
48.0342-2.47985.73768.1738-3.7974.6261-0.1795-0.00891.1711-0.1932-0.2711-0.1736-0.47610.37510.67790.3058-0.08470.04440.3262-0.00730.423833.4836-40.02170.433
53.5182-1.3709-0.15710.68290.27730.1898-0.0404-1.22870.17270.36240.3185-0.45540.04570.4086-0.34810.420.0022-0.07690.6733-0.19910.56157.509-50.74910.8755
67.17260.28482.01163.313-0.89663.8793-0.1297-0.61860.27130.26410.0074-0.81250.00570.46360.05650.328-0.0035-0.06160.4568-0.14810.425167.7198-56.47277.0087
78.0329-0.7357-1.93483.7535-0.06135.5108-0.28110.6848-0.0311-0.65670.27970.89590.0102-0.52590.03370.5058-0.0855-0.15060.37990.11180.525741.5555-24.0326-11.0928
81.35982.84930.35235.96340.84770.272-0.24480.0911-0.3063-0.34860.3313-0.53250.01050.0822-0.08570.3868-0.04880.06340.2841-0.03280.259159.3519-29.5287-2.9267
94.50441.70250.75333.53420.83562.47350.0019-0.0839-0.4350.55270.0339-0.00560.3386-0.0699-0.04950.3418-0.01540.02120.17050.03290.247755.3363-28.72576.5773
105.1778-2.2505-2.82114.81613.3522.7648-0.05840.2811-0.1546-0.5434-0.11981.035-0.2901-0.50880.40750.4407-0.0758-0.04410.31130.0220.510542.135-29.6004-1.8305
110.16090.973-0.04355.7251-0.38260.0110.13750.4899-0.5461-0.54780.4376-0.83410.02150.3838-0.55470.89170.0656-0.03080.4248-0.12950.536255.1936-43.7792-15.6354
121.3251-1.3855-0.40178.90843.36573.10610.03510.2284-0.1717-0.52160.0267-0.0059-0.0710.0604-0.05070.2947-0.04670.03530.3154-0.07450.296259.3537-63.4526-8.5509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 37 )B6 - 37
2X-RAY DIFFRACTION2chain 'B' and (resid 38 through 79 )B38 - 79
3X-RAY DIFFRACTION3chain 'B' and (resid 80 through 147 )B80 - 147
4X-RAY DIFFRACTION4chain 'B' and (resid 148 through 168 )B148 - 168
5X-RAY DIFFRACTION5chain 'B' and (resid 169 through 193 )B169 - 193
6X-RAY DIFFRACTION6chain 'B' and (resid 194 through 241 )B194 - 241
7X-RAY DIFFRACTION7chain 'A' and (resid 6 through 37 )A6 - 37
8X-RAY DIFFRACTION8chain 'A' and (resid 38 through 74 )A38 - 74
9X-RAY DIFFRACTION9chain 'A' and (resid 75 through 144 )A75 - 144
10X-RAY DIFFRACTION10chain 'A' and (resid 145 through 168 )A145 - 168
11X-RAY DIFFRACTION11chain 'A' and (resid 169 through 182 )A169 - 182
12X-RAY DIFFRACTION12chain 'A' and (resid 183 through 241 )A183 - 241

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