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- PDB-6mwz: LasR LBD T75V/Y93F/A127W:BB0126 -

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Basic information

Entry
Database: PDB / ID: 6mwz
TitleLasR LBD T75V/Y93F/A127W:BB0126
Components
  • ALA-HIS-HIS-HIS-HIS-ALA
  • Transcriptional 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-K5M / Transcriptional regulator LasR / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.657 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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator LasR
B: Transcriptional regulator LasR
M: ALA-HIS-HIS-HIS-HIS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9055
Polymers54,2023
Non-polymers7032
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.953, 72.363, 51.872
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator LasR


Mass: 26744.672 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: Protein/peptide ALA-HIS-HIS-HIS-HIS-ALA


Mass: 712.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: UCBPP-PA14 / Gene: poly-His / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-K5M / 4-[3-(methylsulfonyl)phenoxy]-N-[(1S,3S,5S)-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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.55 Å3/Da / Density % sol: 20.9 %
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: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→29.7 Å / Num. obs: 39323 / % possible obs: 99.7 % / Redundancy: 6.8 % / Net I/σ(I): 22.4
Reflection shellResolution: 1.66→1.69 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DPSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.657→29.666 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.53
RfactorNum. reflection% reflection
Rfree0.2374 2093 5.32 %
Rwork0.2073 --
obs0.2089 39323 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.657→29.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 48 77 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062716
X-RAY DIFFRACTIONf_angle_d0.9143687
X-RAY DIFFRACTIONf_dihedral_angle_d17.9151565
X-RAY DIFFRACTIONf_chiral_restr0.053383
X-RAY DIFFRACTIONf_plane_restr0.004469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6572-1.69580.28961280.26132402X-RAY DIFFRACTION97
1.6958-1.73820.3221210.24382524X-RAY DIFFRACTION100
1.7382-1.78520.26211410.2312446X-RAY DIFFRACTION100
1.7852-1.83770.30981350.24142478X-RAY DIFFRACTION100
1.8377-1.8970.29921390.23542480X-RAY DIFFRACTION100
1.897-1.96480.25231430.22992481X-RAY DIFFRACTION100
1.9648-2.04340.26731330.22092502X-RAY DIFFRACTION100
2.0434-2.13640.28991300.21592506X-RAY DIFFRACTION100
2.1364-2.2490.25921360.21632481X-RAY DIFFRACTION100
2.249-2.38990.27661460.2332451X-RAY DIFFRACTION100
2.3899-2.57430.30341500.23252486X-RAY DIFFRACTION100
2.5743-2.83320.24741430.23842483X-RAY DIFFRACTION100
2.8332-3.24270.29571540.22332486X-RAY DIFFRACTION100
3.2427-4.08380.19891410.18762508X-RAY DIFFRACTION100
4.0838-29.67040.18141530.17242516X-RAY DIFFRACTION99

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