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- PDB-6v7w: Crystal structure of LasR-Aqs1 complex from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6v7w
TitleCrystal structure of LasR-Aqs1 complex from Pseudomonas aeruginosa
Components
  • QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
  • Transcriptional regulator LasR
KeywordsDNA BINDING PROTEIN/Viral protein / Prophage protein / quorum sensing / DNA BINDING PROTEIN / DNA BINDING PROTEIN-Viral protein complex
Function / homology
Function and homology information


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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / Transcriptional regulator LasR / Uncharacterized protein / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Pseudomonas virus DMS3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShah, M. / Moraes, T.F. / Maxwell, K.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-136845 Canada
CitationJournal: Mol.Cell / Year: 2021
Title: A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa.
Authors: Shah, M. / Taylor, V.L. / Bona, D. / Tsao, Y. / Stanley, S.Y. / Pimentel-Elardo, S.M. / McCallum, M. / Bondy-Denomy, J. / Howell, P.L. / Nodwell, J.R. / Davidson, A.R. / Moraes, T.F. / Maxwell, K.L.
History
DepositionDec 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Transcriptional regulator LasR
A: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
C: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
E: Transcriptional regulator LasR
D: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
F: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4878
Polymers83,8936
Non-polymers5952
Water19811
1
B: Transcriptional regulator LasR
A: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
C: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2444
Polymers41,9463
Non-polymers2971
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Transcriptional regulator LasR
D: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
F: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2444
Polymers41,9463
Non-polymers2971
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.975, 100.438, 106.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSTHRTHR(chain 'A' and (resid 7 through 30 or resid 36 through 61))AB7 - 297 - 29
121ASNASNARGARG(chain 'A' and (resid 7 through 30 or resid 36 through 61))AB36 - 6136 - 61
211LYSLYSTHRTHR(chain 'C' and resid 7 through 61)CC7 - 297 - 29
221ASNASNARGARG(chain 'C' and resid 7 through 61)CC36 - 6136 - 61
311LYSLYSTHRTHR(chain 'D' and (resid 7 through 30 or resid 36 through 61))DE7 - 297 - 29
321ASNASNARGARG(chain 'D' and (resid 7 through 30 or resid 36 through 61))DE36 - 6136 - 61
411LYSLYSTHRTHR(chain 'F' and (resid 7 through 30 or resid 36 through 61))FF7 - 297 - 29
421ASNASNARGARG(chain 'F' and (resid 7 through 30 or resid 36 through 61))FF36 - 6136 - 61
112PHEPHEILEILEchain 'B'BA7 - 2377 - 237
212PHEPHEILEILE(chain 'E' and resid 7 through 238)ED7 - 2377 - 237

NCS ensembles :
ID
1
2

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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 (bacteria) / References: UniProt: A0A0H2Z901, UniProt: P25084*PLUS
#2: Protein
QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1


Mass: 7649.417 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas virus DMS3 / Gene: DMS3-3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0SML3
#3: Chemical ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium chloride, 0.1M HEPES:NaOH, pH 7.5 and 30% PEG400, 15% glycerol

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→73.11 Å / Num. obs: 21677 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC1/2: 0.998 / Net I/σ(I): 25.4
Reflection shellResolution: 3→3.0381 Å / CC1/2: 1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Cootmodel building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V7U

6v7u


Resolution: 3→73.11 Å / SU ML: 0.4695 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9249
RfactorNum. reflection% reflection
Rfree0.2718 3818 9.39 %
Rwork0.2496 --
obs0.2515 21666 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→73.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 42 11 5480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215583
X-RAY DIFFRACTIONf_angle_d0.60387563
X-RAY DIFFRACTIONf_chiral_restr0.036836
X-RAY DIFFRACTIONf_plane_restr0.0033972
X-RAY DIFFRACTIONf_dihedral_angle_d10.75723323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.040.41751131435X-RAY DIFFRACTION99.87
3.04-3.080.33851491322X-RAY DIFFRACTION99.66
3.08-3.120.39511290.33491395X-RAY DIFFRACTION100
3.12-3.160.36891670.33611325X-RAY DIFFRACTION99.87
3.16-3.210.31681331381X-RAY DIFFRACTION100
3.21-3.260.31531250.30471434X-RAY DIFFRACTION99.87
3.26-3.320.311621285X-RAY DIFFRACTION99.86
3.32-3.370.3441400.29271381X-RAY DIFFRACTION100
3.37-3.430.34961630.3091330X-RAY DIFFRACTION100
3.43-3.50.39071310.30141400X-RAY DIFFRACTION99.87
3.5-3.570.29951470.29531337X-RAY DIFFRACTION99.87
3.57-3.650.3191610.2991343X-RAY DIFFRACTION100
3.65-3.730.28231290.26171388X-RAY DIFFRACTION99.93
3.73-3.830.32271500.27131342X-RAY DIFFRACTION99.93
3.83-3.930.32161300.25861391X-RAY DIFFRACTION99.87
3.93-4.050.32321340.24561368X-RAY DIFFRACTION99.93
4.05-4.180.27291340.25541367X-RAY DIFFRACTION99.87
4.18-4.330.28761580.25061344X-RAY DIFFRACTION100
4.33-4.50.29151300.22861381X-RAY DIFFRACTION99.8
4.5-4.70.23411510.22991357X-RAY DIFFRACTION100
4.7-4.950.2531500.22871345X-RAY DIFFRACTION99.73
4.95-5.260.26351290.22751375X-RAY DIFFRACTION99.93
5.26-5.670.2431621350X-RAY DIFFRACTION100
5.67-6.240.27431350.26121369X-RAY DIFFRACTION100
6.24-7.140.221481371X-RAY DIFFRACTION99.87
7.14-8.990.20991380.19081350X-RAY DIFFRACTION99.6

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