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- PDB-6mww: LasR LBD:BB0126 complex -

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Basic information

Entry
Database: PDB / ID: 6mww
TitleLasR LBD:BB0126 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-K5J / Transcriptional regulator LasR / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.76 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 30, 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)53,9984
Polymers53,2952
Non-polymers7032
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-13 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.892, 63.581, 51.797
Angle α, β, γ (deg.)90.00, 112.17, 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-K5J / 4-[3-(methylsulfonyl)phenoxy]-N-[(1R,3R,5R)-2-oxobicyclo[3.1.0]hexan-3-yl]butanamide


Mass: 351.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO5S / Feature type: SUBJECT OF INVESTIGATION

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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: 1.46 Å3/Da / Density % sol: 15.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, 30% PEG400

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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: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→23.8 Å / Num. obs: 7739 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 62.45 Å2 / Net I/σ(I): 7.6
Reflection shellResolution: 2.76→2.86 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.76→23.78 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.785 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.439
RfactorNum. reflection% reflectionSelection details
Rfree0.281 401 5.18 %RANDOM
Rwork0.204 ---
obs0.208 7739 97.2 %-
Displacement parametersBiso mean: 38.12 Å2
Baniso -1Baniso -2Baniso -3
1--15.401 Å20 Å2-5.3045 Å2
2--6.0756 Å20 Å2
3---9.3254 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.76→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 48 0 2624
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012770HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153809HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d926SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes405HARMONIC5
X-RAY DIFFRACTIONt_it2770HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion23.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion333SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3116SEMIHARMONIC4
LS refinement shellResolution: 2.76→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.274 115 5.62 %
Rwork0.231 1932 -
all0.234 2047 -
obs--91.62 %

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