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- PDB-7r3h: PROSS optimitzed variant of RhlR (75 mutations) in complex with n... -

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Basic information

Entry
Database: PDB / ID: 7r3h
TitlePROSS optimitzed variant of RhlR (75 mutations) in complex with native autoinducer C4-HSL
ComponentsPROSS optimized variant of RhlR with 75 mutations
KeywordsTRANSCRIPTION / QUORUM SENSING / LuxR-type TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / DNA BINDING PROTEIN / GENE REGULATION / mBTL / rhamnolipid
Function / homologyN-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 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
B: PROSS optimized variant of RhlR with 75 mutations
A: PROSS optimized variant of RhlR with 75 mutations
C: PROSS optimized variant of RhlR with 75 mutations
D: PROSS optimized variant of RhlR with 75 mutations
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5336
Polymers111,1904
Non-polymers3422
Water00
1
B: PROSS optimized variant of RhlR with 75 mutations
A: PROSS optimized variant of RhlR with 75 mutations
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9384
Polymers55,5952
Non-polymers3422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-20 kcal/mol
Surface area20500 Å2
MethodPISA
2
C: PROSS optimized variant of RhlR with 75 mutations
D: PROSS optimized variant of RhlR with 75 mutations


Theoretical massNumber of molelcules
Total (without water)55,5952
Polymers55,5952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-21 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.952, 91.560, 117.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PROSS optimized variant of RhlR with 75 mutations


Mass: 27797.574 Da / Num. of mol.: 4
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) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone


Mass: 171.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO3 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaSCN, 20 % (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: 3.49→72.18 Å / Num. obs: 12584 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 82.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.101 / Rrim(I) all: 0.365 / Net I/σ(I): 8 / Num. measured all: 161488
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
3.49-3.6813.51.4592432218040.7610.4091.5162.5100
11.04-72.1811.40.0652584620.9980.0180.06326.799.7

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted structure of RhlR with phyre2

Resolution: 3.49→70.37 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 594 4.74 %
Rwork0.2227 11942 -
obs0.225 12536 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 198.72 Å2 / Biso mean: 85.7799 Å2 / Biso min: 37.43 Å2
Refinement stepCycle: final / Resolution: 3.49→70.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 50 0 7328
Biso mean--108.21 --
Num. residues----941
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.49-3.840.32031420.263229383080
3.84-4.40.29861430.232629303073
4.4-5.540.25931490.221929803129
5.54-70.370.24081600.201730943254
Refinement TLS params.Method: refined / Origin x: 41.242 Å / Origin y: -5.1102 Å / Origin z: 9.7514 Å
111213212223313233
T0.4522 Å20.0053 Å2-0.0153 Å2-0.4464 Å2-0.0017 Å2--0.451 Å2
L0.1652 °2-0.1332 °20.0477 °2-0.1148 °2-0.033 °2--0.0276 °2
S-0.0791 Å °-0.0299 Å °0.0881 Å °-0.0063 Å °0.0237 Å °0.0791 Å °-0.0073 Å °0.0164 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB6 - 241
2X-RAY DIFFRACTION1allB301
3X-RAY DIFFRACTION1allA6 - 241
4X-RAY DIFFRACTION1allA301
5X-RAY DIFFRACTION1allC5 - 241
6X-RAY DIFFRACTION1allD6 - 241

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