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- PDB-6h56: Effector domain of Pseudomonas aeruginosa VgrG2b -

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Basic information

Entry
Database: PDB / ID: 6h56
TitleEffector domain of Pseudomonas aeruginosa VgrG2b
ComponentsEffector domain of Pseudomonas aeruginosa VgrG2b
KeywordsMETAL BINDING PROTEIN / Zn binding / T6SS / effector
Function / homology
Function and homology information


type VI protein secretion system complex / protein secretion by the type VI secretion system / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / hydrolase activity / extracellular region / metal ion binding
Similarity search - Function
Type VI secretion system spike protein VgrG2, C-terminal domain of unknown function DUF2345 / Putative type VI secretion system, Rhs element associated Vgr domain / Uncharacterized protein conserved in bacteria (DUF2345) / Putative type VI secretion system Rhs element Vgr / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Type VI secretion system spike protein VgrG2b
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsForster, A. / Freemont, P.S. / Filloux, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K001930/1 United Kingdom
CitationJournal: Cell Rep / Year: 2019
Title: The Pseudomonas aeruginosa T6SS Delivers a Periplasmic Toxin that Disrupts Bacterial Cell Morphology.
Authors: Wood, T.E. / Howard, S.A. / Forster, A. / Nolan, L.M. / Manoli, E. / Bullen, N.P. / Yau, H.C.L. / Hachani, A. / Hayward, R.D. / Whitney, J.C. / Vollmer, W. / Freemont, P.S. / Filloux, A.
History
DepositionJul 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
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 / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Effector domain of Pseudomonas aeruginosa VgrG2b
B: Effector domain of Pseudomonas aeruginosa VgrG2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4074
Polymers55,2762
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS shows both monomers and dimers in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-78 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.310, 78.310, 115.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Effector domain of Pseudomonas aeruginosa VgrG2b


Mass: 27638.010 Da / Num. of mol.: 2 / Mutation: E995A K996A E998A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0262 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q9I6M7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M bis-tris, 45% polypropylene glycol P400

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0410.97949
SYNCHROTRONDiamond I0220.97949
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 17, 2014
DECTRIS PILATUS 6M-F2PIXELJun 24, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
21
ReflectionResolution: 3.2→43.93 Å / Num. obs: 12896 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 123.51 Å2 / Rrim(I) all: 0.09 / Net I/σ(I): 10.9
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / Rrim(I) all: 0.757 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→43.93 Å / Cor.coef. Fo:Fc: 0.9279 / Cor.coef. Fo:Fc free: 0.9332 / SU R Cruickshank DPI: 0.86 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.684 / SU Rfree Blow DPI: 0.325 / SU Rfree Cruickshank DPI: 0.344
RfactorNum. reflection% reflectionSelection details
Rfree0.232 644 5 %RANDOM
Rwork0.2233 ---
obs0.2238 12887 98.69 %-
Displacement parametersBiso mean: 115.36 Å2
Baniso -1Baniso -2Baniso -3
1-4.2724 Å20 Å20 Å2
2--4.2724 Å20 Å2
3----8.5447 Å2
Refine analyzeLuzzati coordinate error obs: 0.914 Å
Refinement stepCycle: 1 / Resolution: 3.2→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 2 0 2745
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013796HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d941SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes422HARMONIC5
X-RAY DIFFRACTIONt_it2802HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion20.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion338SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3186SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.5 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2794 150 4.87 %
Rwork0.2712 2933 -
all0.2716 3083 -
obs--98.69 %
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)
16.9531-0.69612.29752.91450.826.56-0.36630.02060.014-0.02090.65270.17840.0750.1963-0.2863-0.3061-0.14830.03620.2161-0.1101-0.3040.024737.038554.146
29.0770.76841.29251.46840.61946.1576-0.01570.1567-0.4280.0773-0.4921-0.28010.1941-0.10930.5078-0.39460.00490.1002-0.0493-0.1176-0.095141.385927.875557.0116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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