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- PDB-7r3i: PROSS optimitzed variant of RhlR (61 mutations) in complex with t... -

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Basic information

Entry
Database: PDB / ID: 7r3i
TitlePROSS optimitzed variant of RhlR (61 mutations) in complex with the synthetic antagonist mBTL
ComponentsPROSS optimized variant of RhlR with 61 mutations
KeywordsTRANSCRIPTION / QUORUM SENSING / LuxR-type TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / DNA BINDING PROTEIN / GENE REGULATION / mBTL / rhamnolipid
Function / homologyChem-K5G
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
Revision 1.1May 1, 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

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Assembly

Deposited unit
A: PROSS optimized variant of RhlR with 61 mutations
B: PROSS optimized variant of RhlR with 61 mutations
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1894
Polymers55,4732
Non-polymers7172
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-18 kcal/mol
Surface area21860 Å2
Unit cell
Length a, b, c (Å)85.904, 85.904, 202.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROSS optimized variant of RhlR with 61 mutations


Mass: 27736.342 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Escherichia coli (E. coli)
#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
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: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM BICINE pH 8.8, 8.6 % (w/v) PEG 2K, 17.1 % (v/v) PEG MME 350 3 mg/ml 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: Oct 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→43.63 Å / Num. obs: 14516 / % possible obs: 100 % / Redundancy: 25.2 % / Biso Wilson estimate: 84.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.026 / Rrim(I) all: 0.131 / Net I/σ(I): 21.9 / Num. measured all: 365564 / 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
3.1-3.3126.70.8466818825570.9440.1660.8625.3100
8.77-43.6319.40.048144677450.9990.0110.0552.799.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.19.2refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure prediction of RhlR with phyre2

Resolution: 3.1→43.63 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 689 4.77 %
Rwork0.2479 13765 -
obs0.2492 14454 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.2 Å2 / Biso mean: 101.3718 Å2 / Biso min: 48.5 Å2
Refinement stepCycle: final / Resolution: 3.1→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 72 0 3646
Biso mean--80.36 --
Num. residues----471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.340.34641260.296326732799
3.34-3.670.30031530.293426762829
3.68-4.210.25771350.234527222857
4.21-5.30.26431270.230327712898
5.3-43.630.26141480.241329233071
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)
10.0324-0.0094-0.02090.01030.010.0262-0.0714-0.22150.06620.0490.1443-0.10770.07660.10960.01720.91430.21050.35671.00790.07871.529931.9756.879195.5893
20.0069-0.009-0.00530.0140.00730.0651-0.0329-0.1389-0.11630.0535-0.0969-0.08610.1420.0476-0.01531.2289-0.13660.2620.60290.24851.215322.059853.149596.7033
30.3832-0.2135-0.2930.15970.16960.22260.17370.3222-0.1416-0.3467-0.1593-0.08870.1791-0.1404-0.01020.563-0.3164-0.23780.52950.13390.679.161962.382893.2607
40.02110.0274-0.03370.0341-0.02990.01650.2514-0.04020.08-0.1340.12390.0008-0.0299-0.10660.00010.7422-0.2347-0.29010.64590.18171.00826.910769.44798.9681
50.12010.0582-0.08760.0748-0.05990.1062-0.4015-0.2480.25360.4542-0.2288-0.5465-0.46920.1577-0.42560.6783-0.3007-0.2890.46730.30180.71978.858164.5943104.1958
60.12460.09120.03580.03260.0210.0982-0.1194-0.22920.15760.0269-0.1641-0.2037-0.15870.1416-0.22880.3237-0.9108-0.6010.72020.45040.92123.689464.5801102.5313
70.009-0.0118-0.00240.00690.00770.0071-0.07580.08410.0554-0.0972-0.02570.0085-0.15420.0358-01.0992-0.24220.18190.734-0.00720.711419.710670.412278.5744
80.02650.027-0.01410.024400.03090.11250.07020.30870.10960.030.04590.0329-0.210700.6332-0.0540.02830.69010.34850.719318.380596.902674.8108
90.17790.1634-0.11130.2517-0.07350.0928-0.28820.0457-0.1811-0.28720.0876-0.1555-0.1490.14780.00810.6718-0.2216-0.0670.96230.34450.363112.734287.394273.2384
100.1922-0.0424-0.16940.030.03390.11390.2774-0.7262-0.5220.2102-0.2791-0.24380.1885-0.18320.07330.7791-0.3291-0.27580.73420.39380.70732.785284.367104.8816
110.2506-0.01860.10490.0794-0.05180.1309-0.31420.7353-0.3604-0.6570.28670.0706-0.02550.3260.02650.7029-0.3051-0.16910.67590.15870.726138.920485.291690.8132
120.1462-0.0361-0.07370.03710.04750.0929-0.1408-0.0305-0.3082-0.31260.0464-0.3142-0.0941-0.1284-0.32240.5223-0.4612-0.08550.28110.62551.10132.926575.3906102.0786
130.087-0.0277-0.05520.0297-0.02250.04550.14130.08250.141-0.03730.06920.2491-0.0224-0.61560.04270.6281-0.1670.01581.02560.20430.52942.917189.7388.8276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 23 )A7 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 37 )A24 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 72 )A38 - 72
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 95 )A73 - 95
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 144 )A96 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 167 )A145 - 167
7X-RAY DIFFRACTION7chain 'A' and (resid 168 through 182 )A168 - 182
8X-RAY DIFFRACTION8chain 'A' and (resid 183 through 208 )A183 - 208
9X-RAY DIFFRACTION9chain 'A' and (resid 209 through 241 )A209 - 241
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 65 )B6 - 65
11X-RAY DIFFRACTION11chain 'B' and (resid 66 through 144 )B66 - 144
12X-RAY DIFFRACTION12chain 'B' and (resid 145 through 168 )B145 - 168
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 241 )B169 - 241

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