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- PDB-6v7v: Structure of a phage-encoded quorum sensing anti-activator, Aqs1 -

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Basic information

Entry
Database: PDB / ID: 6v7v
TitleStructure of a phage-encoded quorum sensing anti-activator, Aqs1
ComponentsQuorum sensing anti-activator Aqs1
KeywordsVIRAL PROTEIN / Prophage protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas virus DMS3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
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: Quorum sensing anti-activator Aqs1
B: Quorum sensing anti-activator Aqs1
C: Quorum sensing anti-activator Aqs1
D: Quorum sensing anti-activator Aqs1
E: Quorum sensing anti-activator Aqs1
F: Quorum sensing anti-activator Aqs1


Theoretical massNumber of molelcules
Total (without water)45,2006
Polymers45,2006
Non-polymers00
Water1,802100
1
A: Quorum sensing anti-activator Aqs1
B: Quorum sensing anti-activator Aqs1


Theoretical massNumber of molelcules
Total (without water)15,0672
Polymers15,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-16 kcal/mol
Surface area7320 Å2
MethodPISA
2
C: Quorum sensing anti-activator Aqs1
D: Quorum sensing anti-activator Aqs1


Theoretical massNumber of molelcules
Total (without water)15,0672
Polymers15,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-16 kcal/mol
Surface area7300 Å2
MethodPISA
3
E: Quorum sensing anti-activator Aqs1
F: Quorum sensing anti-activator Aqs1


Theoretical massNumber of molelcules
Total (without water)15,0672
Polymers15,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.730, 66.120, 73.210
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Quorum sensing anti-activator Aqs1


Mass: 7533.278 Da / Num. of mol.: 6 / Mutation: K24A, E25A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M tri-sodium citrate, pH 5.5, 15% ethanol, 0.2M lithium sulphate and 15% glycerol

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→45.17 Å / Num. obs: 24477 / % possible obs: 98.91 % / Redundancy: 1.9 % / Biso Wilson estimate: 29.27 Å2 / CC1/2: 0.9 / Net I/σ(I): 1.92
Reflection shellResolution: 2.3→2.3822 Å / Num. unique obs: 2419 / CC1/2: 0.5 / % possible all: 98

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Processing

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

6v7u


Resolution: 2.3→45.17 Å / SU ML: 0.279 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.23
RfactorNum. reflection% reflection
Rfree0.244 1221 4.98 %
Rwork0.205 --
obs0.207 24440 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 0 100 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062776
X-RAY DIFFRACTIONf_angle_d0.7843777
X-RAY DIFFRACTIONf_dihedral_angle_d8.1111667
X-RAY DIFFRACTIONf_chiral_restr0.039446
X-RAY DIFFRACTIONf_plane_restr0.005486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.33721380.30572667X-RAY DIFFRACTION98
2.35-2.40.31451340.27052619X-RAY DIFFRACTION98
2.4-2.450.30421390.27112608X-RAY DIFFRACTION98
2.45-2.520.331390.27082613X-RAY DIFFRACTION98
2.52-2.580.27231300.2382591X-RAY DIFFRACTION99
2.58-2.660.2981420.24482696X-RAY DIFFRACTION99
2.66-2.750.26361410.23242644X-RAY DIFFRACTION98
2.75-2.840.27821360.23822567X-RAY DIFFRACTION99
2.84-2.960.25061400.23282669X-RAY DIFFRACTION99
2.96-3.090.28911420.22682696X-RAY DIFFRACTION99
3.09-3.250.2741380.22782580X-RAY DIFFRACTION99
3.25-3.460.21991440.21072669X-RAY DIFFRACTION99
3.46-3.730.25831410.1822684X-RAY DIFFRACTION100
3.73-4.10.20171390.16672686X-RAY DIFFRACTION99
4.1-4.690.19621380.16222648X-RAY DIFFRACTION100
4.69-5.910.19181350.17642643X-RAY DIFFRACTION100
5.91-45.170.21071390.16812674X-RAY DIFFRACTION99
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)
11.89611.8762-1.10894.9159-2.61454.6070.1581-0.14420.12720.1459-0.2483-0.1094-0.49450.44440.05930.2847-0.0302-0.02560.2495-0.01080.1597-20.8851-36.733350.0664
27.5365-2.84531.26127.6117-2.23824.28770.04790.24780.01-0.1415-0.0813-0.0522-0.07660.22890.03230.3383-0.0374-0.00050.26350.00010.1001-20.4988-33.752139.2886
34.2718-3.6552-1.55834.53781.29333.272-0.02570.1291-0.23210.137-0.07590.02580.5080.13610.10050.3690.0069-0.00270.25870.03590.153-21.4406-29.954725.5922
47.59320.1319-3.32382.56470.27336.3795-0.01150.07890.1579-0.02060.0570.07170.3842-0.1734-0.04670.30620.03640.00040.2268-0.01210.1246-18.9111-31.192314.7948
53.01161.29571.59190.95350.79354.3936-0.2391-0.38510.1536-0.07280.04990.1113-0.1281-0.68070.15080.29660.0210.01710.2873-0.01740.1736-15.2442-32.56171.2074
65.36623.59171.86845.49422.25656.6403-0.15840.0653-0.04310.12140.2144-0.0996-0.071-0.0062-0.0220.22930.0155-0.02230.2657-0.01070.1061-17.6342-34.1843-9.516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:63)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 1:62)
3X-RAY DIFFRACTION3(CHAIN C AND RESID 1:62)
4X-RAY DIFFRACTION4(CHAIN D AND RESID 2:62)
5X-RAY DIFFRACTION5(CHAIN E AND RESID 1:62)
6X-RAY DIFFRACTION6(CHAIN F AND RESID 2:62)

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