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- PDB-6mwl: LasR LBD:mBTL complex -

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Basic information

Entry
Database: PDB / ID: 6mwl
TitleLasR LBD:mBTL complex
ComponentsTranscriptional regulator LasR
KeywordsTRANSCRIPTION / Transcriptional activator
Function / homology
Function and homology information


positive regulation of elastin biosynthetic process / regulation of elastin catabolic process / quorum sensing / DNA-binding transcription activator activity / protein-DNA complex / regulation of gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription ...positive regulation of elastin biosynthetic process / regulation of elastin catabolic process / quorum sensing / DNA-binding transcription activator activity / protein-DNA complex / regulation of gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive 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
Chem-K5G / Transcriptional regulator LasR / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsBassler, B.L. / Paczkowski, J.E.
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
CitationJournal: 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.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)54,0124
Polymers53,2952
Non-polymers7172
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-15 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.073, 67.325, 53.785
Angle α, β, γ (deg.)90.00, 117.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator LasR


Mass: 26647.514 Da / Num. of mol.: 2
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, UniProt: P25084*PLUS
#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.: 276 / 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: 1.58 Å3/Da / Density % sol: 21.92 %
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: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→20.2 Å / Num. obs: 52957 / % possible obs: 99.1 % / Redundancy: 3.4 % / Net I/σ(I): 18.5
Reflection shellResolution: 1.5→1.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.5→20.2 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.54
RfactorNum. reflection% reflection
Rfree0.2215 2670 5.09 %
Rwork0.1909 --
obs0.1924 52448 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→20.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 40 276 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072666
X-RAY DIFFRACTIONf_angle_d1.143612
X-RAY DIFFRACTIONf_dihedral_angle_d16.986966
X-RAY DIFFRACTIONf_chiral_restr0.072376
X-RAY DIFFRACTIONf_plane_restr0.004466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.52730.3851010.37132339X-RAY DIFFRACTION87
1.5273-1.55670.30931140.29522587X-RAY DIFFRACTION99
1.5567-1.58850.26851390.2522644X-RAY DIFFRACTION99
1.5885-1.6230.26541720.24312585X-RAY DIFFRACTION100
1.623-1.66070.25461410.22992589X-RAY DIFFRACTION100
1.6607-1.70220.26151290.22862647X-RAY DIFFRACTION100
1.7022-1.74820.27231360.2272635X-RAY DIFFRACTION99
1.7482-1.79960.22181430.18872644X-RAY DIFFRACTION100
1.7996-1.85770.24321510.18792628X-RAY DIFFRACTION100
1.8577-1.9240.20311370.18332626X-RAY DIFFRACTION100
1.924-2.0010.22841360.18542629X-RAY DIFFRACTION100
2.001-2.0920.19751310.1912650X-RAY DIFFRACTION100
2.092-2.20220.23571320.17442640X-RAY DIFFRACTION100
2.2022-2.33990.23211640.18622634X-RAY DIFFRACTION100
2.3399-2.52030.21461450.19272632X-RAY DIFFRACTION100
2.5203-2.77330.18281500.19572662X-RAY DIFFRACTION100
2.7733-3.17330.23371640.19652627X-RAY DIFFRACTION100
3.1733-3.9930.23311480.1692667X-RAY DIFFRACTION100
3.993-20.20190.18211370.17192713X-RAY DIFFRACTION100

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