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- PDB-6mvm: LasR LBD L130F:3OC14HSL complex -

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Basic information

Entry
Database: PDB / ID: 6mvm
TitleLasR LBD L130F:3OC14HSL complex
ComponentsTranscriptional regulator LasR
KeywordsTRANSCRIPTION / transcriptional activator protein / 3-Oxo-N-(2-oxooxolan-3-yl)tetradecanamide
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
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 / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxo-N-[(3S)-2-oxooxolan-3-yl]tetradecanamide / Transcriptional regulator LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsPaczkowski, J.E. / Bassler, B.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R37GM065859 United States
National Science Foundation (NSF, United States)MCB-1713731 United States
Howard Hughes Medical Institute (HHMI) United States
Citation
Journal: Acs Chem.Biol. / Year: 2019
Title: An Autoinducer Analogue Reveals an Alternative Mode of Ligand Binding for the LasR Quorum-Sensing Receptor.
Authors: Paczkowski, J.E. / McCready, A.R. / Cong, J.P. / Li, Z. / Jeffrey, P.D. / Smith, C.D. / Henke, B.R. / Hughson, F.M. / Bassler, B.L.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural determinants driving homoserine lactone ligand selection in thePseudomonas aeruginosaLasR quorum-sensing receptor.
Authors: McCready, A.R. / Paczkowski, J.E. / Henke, B.R. / Bassler, B.L.
History
DepositionOct 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator LasR
B: Transcriptional regulator LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0924
Polymers36,4412
Non-polymers6512
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.881, 70.774, 53.817
Angle α, β, γ (deg.)90.00, 90.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator LasR


Mass: 18220.516 Da / Num. of mol.: 2 / Fragment: UNP residues 7-168 / Mutation: L130F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: lasR, PA14_45960 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z901
#2: Chemical ChemComp-K4G / 3-oxo-N-[(3S)-2-oxooxolan-3-yl]tetradecanamide


Mass: 325.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H31NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200 mM magnesium nitrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.895→30 Å / Num. obs: 25887 / % possible obs: 96.6 % / Redundancy: 2.5 % / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.98 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2UV0

2uv0


Resolution: 1.895→29.568 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.58
RfactorNum. reflection% reflection
Rfree0.2654 1292 4.99 %
Rwork0.2131 --
obs0.2231 25887 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.895→29.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 46 127 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072688
X-RAY DIFFRACTIONf_angle_d1.0213632
X-RAY DIFFRACTIONf_dihedral_angle_d17.882978
X-RAY DIFFRACTIONf_chiral_restr0.037374
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-1.97670.48691310.39542545X-RAY DIFFRACTION86
1.9767-2.06650.41161330.32652720X-RAY DIFFRACTION92
2.0665-2.17530.34351380.28812731X-RAY DIFFRACTION93
2.1753-2.31120.29531470.26132709X-RAY DIFFRACTION93
2.3112-2.48920.30251590.25562772X-RAY DIFFRACTION93
2.4892-2.73870.31141580.24172712X-RAY DIFFRACTION93
2.7387-3.13270.29081180.2232775X-RAY DIFFRACTION94
3.1327-3.93850.22621450.17992779X-RAY DIFFRACTION94
3.9385-16.76570.22241230.17192808X-RAY DIFFRACTION93

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