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- PDB-6v7u: Structure of a phage-encoded quorum sensing anti-activator, Aqs1 -

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Basic information

Entry
Database: PDB / ID: 6v7u
TitleStructure of a phage-encoded quorum sensing anti-activator, Aqs1
ComponentsQuorum sensing anti-activator protein Aqs1
KeywordsVIRAL PROTEIN / Prophage protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPseudomonas virus DMS3
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 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 1.2Mar 6, 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: Quorum sensing anti-activator protein Aqs1
B: Quorum sensing anti-activator protein Aqs1


Theoretical massNumber of molelcules
Total (without water)15,0672
Polymers15,0672
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-15 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.410, 66.410, 73.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Quorum sensing anti-activator protein Aqs1


Mass: 7533.278 Da / Num. of mol.: 2 / 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.: 45 / 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: 3.05 Å3/Da / Density % sol: 59.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1M NaH2PO4/K2HPO4, pH 5.6 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: 2.08→45.25 Å / Num. obs: 12983 / % possible obs: 99.49 % / Redundancy: 10.8 % / Biso Wilson estimate: 27.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.81
Reflection shellResolution: 2.08→2.2895 Å / Num. unique obs: 1290 / CC1/2: 0.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDS1.14_3260data scaling
PHENIXphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.08→45.25 Å / SU ML: 0.2037 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 27.521
RfactorNum. reflection% reflection
Rfree0.2574 1191 4.89 %
Rwork0.2134 --
obs0.2156 12960 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.13 Å2
Refinement stepCycle: LAST / Resolution: 2.08→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms932 0 0 45 977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058945
X-RAY DIFFRACTIONf_angle_d0.69251285
X-RAY DIFFRACTIONf_chiral_restr0.0353152
X-RAY DIFFRACTIONf_plane_restr0.0037165
X-RAY DIFFRACTIONf_dihedral_angle_d8.1324569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.170.30541320.26882537X-RAY DIFFRACTION99.11
2.17-2.290.25261390.24192589X-RAY DIFFRACTION99.34
2.29-2.430.27041320.23672553X-RAY DIFFRACTION99.59
2.43-2.620.28761250.22222595X-RAY DIFFRACTION99.38
2.62-2.880.27231360.22032568X-RAY DIFFRACTION99.74
2.88-3.30.28241270.22142575X-RAY DIFFRACTION99.74
3.3-4.160.24111350.18852574X-RAY DIFFRACTION99.96
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)
16.8200018792-1.750973448692.188839659712.37184018995-0.1836041148033.46153357821-0.219981311963-0.09453454159720.1648486153360.1808412714460.06393779272750.146925798638-0.437991835405-0.3753162399550.1452662163760.3463569555270.04712261038830.0111286400190.289583904256-0.03163100737880.08507932240423.6564307521636.617712451637.7420426951
27.19169626562.792951551692.749318199294.303927556430.5693744138187.41114011118-0.1189470740650.174744645192-0.125572321232-0.1214952256020.0358016343528-0.135595074746-0.1426861107580.1075437094470.0387893666840.2396425848420.0748859049944-0.002518294952510.2879141044150.01022536987570.08654037263160.94582454130335.830397747626.9366425112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:63)
2X-RAY DIFFRACTION2(chain B and resid 4:62)

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