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- PDB-6h8f: Fragment of the C-terminal domain of the TssA component of the ty... -

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Basic information

Entry
Database: PDB / ID: 6h8f
TitleFragment of the C-terminal domain of the TssA component of the type VI secretion system from Burkholderia cenocepacia
ComponentsTssA
KeywordsTRANSPORT PROTEIN / alpha-helical protein / type VI secretion system component / TssA
Function / homologyType VI secretion system protein TssA-like / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / metal ion binding / Type VI secretion protein ImpA
Function and homology information
Biological speciesBurkholderia cenocepacia H111 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsDix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. ...Dix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / Bullough, P.A. / Rice, D.W. / Thomas, M.S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014443/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/F016840/1 United Kingdom
Higher Education Funding Council for England (HEFCE)R/151699 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural insights into the function of type VI secretion system TssA subunits.
Authors: Dix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / ...Authors: Dix, S.R. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Brooker, T.A. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / Bullough, P.A. / Rice, D.W. / Thomas, M.S.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 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: TssA
B: TssA


Theoretical massNumber of molelcules
Total (without water)17,1852
Polymers17,1852
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-23 kcal/mol
Surface area6230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 62.700, 65.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein TssA / Type VI secretion system protein ImpA


Mass: 8592.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Purification by maltose binding protein cleaved after IEGRRemaining tag residues ISHM-299-302Construct comprises residues 303-373 of 1-373
Source: (gene. exp.) Burkholderia cenocepacia H111 (bacteria)
Gene: I35_RS01755 / Plasmid: pMAL-c5X / Production host: Escherichia coli (E. coli) / Variant (production host): NEB Express / References: UniProt: A0A1V2W6E8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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

Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid pH 5.0, 20 % (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.78→38.9 Å / Num. obs: 9502 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.039 / Net I/σ(I): 13.2
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 0.697 / Num. measured obs: 3268 / Num. unique all: 700 / Rpim(I) all: 0.387

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.78→38.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.105 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23729 454 4.8 %RANDOM
Rwork0.18891 ---
obs0.19118 9048 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.312 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2---1.08 Å20 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.78→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 39 791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019774
X-RAY DIFFRACTIONr_bond_other_d0.0010.02727
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9151054
X-RAY DIFFRACTIONr_angle_other_deg0.91331655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.263589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54222.85742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55415121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.955158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2852.088362
X-RAY DIFFRACTIONr_mcbond_other5.2842.085361
X-RAY DIFFRACTIONr_mcangle_it6.0413.081449
X-RAY DIFFRACTIONr_mcangle_other6.0343.084450
X-RAY DIFFRACTIONr_scbond_it42.753.128411
X-RAY DIFFRACTIONr_scbond_other42.753.129411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other30.9494.233605
X-RAY DIFFRACTIONr_long_range_B_refined26.27419.349916
X-RAY DIFFRACTIONr_long_range_B_other26.47519.163901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 30 -
Rwork0.272 668 -
obs--98.87 %

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