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- PDB-6v7x: Structure of a phage-encoded quorum sensing anti-activator, Aqs1 ... -

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Basic information

Entry
Database: PDB / ID: 6v7x
TitleStructure of a phage-encoded quorum sensing anti-activator, Aqs1 bound to LasR
Components
  • QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
  • Transcriptional regulator LasR
KeywordsDNA BINDING PROTEIN/Viral protein / Prophage protein / VIRAL 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 virus DMS3
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
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: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
B: Transcriptional regulator LasR
C: QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2444
Polymers41,9463
Non-polymers2971
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.536, 104.536, 102.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein QUORUM SENSING ANTI-ACTIVATOR PROTEIN AQS1


Mass: 7649.417 Da / Num. of mol.: 2
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
#2: Protein Transcriptional regulator LasR


Mass: 26647.514 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.34 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6M ammonium sulfate, 0.1M MES NAOH, pH 6.5 and 10% Dioxane

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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: 2.9→73.92 Å / Num. obs: 13116 / % possible obs: 99.88 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 31.89
Reflection shellResolution: 2.9001→3.0038 Å / Num. unique obs: 24035 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Cootmodel building
XSCALEdata scaling
PHENIXphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IX3

3ix3


Resolution: 2.9→73.92 Å / SU ML: 0.4565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2082
RfactorNum. reflection% reflection
Rfree0.2806 2374 9.88 %
Rwork0.2491 --
obs-13107 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→73.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 21 28 2702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372730
X-RAY DIFFRACTIONf_angle_d0.69593697
X-RAY DIFFRACTIONf_chiral_restr0.0413408
X-RAY DIFFRACTIONf_plane_restr0.0043474
X-RAY DIFFRACTIONf_dihedral_angle_d12.58251622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.960.39691391248X-RAY DIFFRACTION99.36
2.96-3.020.3491351272X-RAY DIFFRACTION99.79
3.02-3.090.44851431290X-RAY DIFFRACTION100
3.09-3.170.32541411265X-RAY DIFFRACTION99.72
3.17-3.260.3081541263X-RAY DIFFRACTION100
3.26-3.350.27811451263X-RAY DIFFRACTION100
3.35-3.460.31511320.28451289X-RAY DIFFRACTION99.86
3.46-3.580.35861370.29451282X-RAY DIFFRACTION99.79
3.58-3.730.34381480.28441246X-RAY DIFFRACTION100
3.73-3.90.281410.25571282X-RAY DIFFRACTION99.86
3.9-4.10.2931410.24881289X-RAY DIFFRACTION100
4.1-4.360.24441331263X-RAY DIFFRACTION100
4.36-4.70.27041360.22141284X-RAY DIFFRACTION100
4.7-5.170.25771390.23351287X-RAY DIFFRACTION100
5.17-5.920.29181260.23331281X-RAY DIFFRACTION100
5.91-7.450.24981350.1951284X-RAY DIFFRACTION99.86
5.92-7.450.24651490.23871273X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.393718641272.66712387945-1.956853892674.695298301632.017469383437.52066129736-0.04922194463661.046670572680.113150343727-1.07133242248-0.0230047929725-0.0261350305419-1.21419009954-0.0916822126068-0.1084758869851.18066998770.0887518385692-0.1274270893861.464770673280.1569275849740.99707490123516.92696913921.1313185203-42.499622955
22.722119006290.370281264736-1.079032469942.049483523610.2843865003916.925861699-0.09694712513090.278990274553-0.1243582911080.07888074402540.138542709342-0.1380761396830.9124288914060.1608285910950.009791030701170.626073254167-0.0142374011181-0.1014213739620.548127548719-0.04984487464270.89207419345523.28903928763.53901922449-12.7963879195
32.28206178762-0.3279333731081.537352293195.443290043492.165682309147.371033918860.186881709801-0.1215344968960.7745465462781.53063506230.751352828014-0.200327880188-0.0395528850879-0.919232104126-0.4417090947261.397689031940.336578319460.09490881906021.500290468970.2209280906151.2828133430915.017644023322.5854513033-30.0051397416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:61)
2X-RAY DIFFRACTION2(chain B and resid 21:238)
3X-RAY DIFFRACTION3(chain C and resid 7:60)

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