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- PDB-6h8e: Truncated derivative of the C-terminal domain of the TssA compone... -

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Basic information

Entry
Database: PDB / ID: 6h8e
TitleTruncated derivative of the C-terminal domain of the TssA component of the type VI secretion system from Burkholderia cenocepacia
ComponentsType VI secretion protein ImpA
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 / MOLECULAR REPLACEMENT / Resolution: 2.35 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 EnglandR/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 1.1Jan 17, 2024Group: 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: Type VI secretion protein ImpA
B: Type VI secretion protein ImpA


Theoretical massNumber of molelcules
Total (without water)15,7502
Polymers15,7502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-19 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.280, 65.280, 66.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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


Mass: 7874.806 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Purification by maltose binding protein cleaved after IEGR, followed by 6His tagRemaining tag residues ISHMSSHHHHHH-291-302Construct comprises residues 303-358 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

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.18 M tri-ammonium citrate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.35→42.97 Å / Num. obs: 6747 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.037 / Net I/σ(I): 17.1
Reflection shellResolution: 2.35→2.41 Å / Rmerge(I) obs: 0.713 / Num. measured obs: 4002 / Num. unique all: 492 / Rpim(I) all: 0.286

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H8F

6h8f


Resolution: 2.35→42.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.501 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.213 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23694 357 5.3 %RANDOM
Rwork0.19307 ---
obs0.19543 6372 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.245 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20.74 Å20 Å2
2--1.48 Å20 Å2
3----4.8 Å2
Refinement stepCycle: 1 / Resolution: 2.35→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 0 0 897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019921
X-RAY DIFFRACTIONr_bond_other_d0.0010.02868
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9191253
X-RAY DIFFRACTIONr_angle_other_deg0.97231984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99723.46949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26915148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.084158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02228
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_it3.1094.056438
X-RAY DIFFRACTIONr_mcbond_other3.1094.047437
X-RAY DIFFRACTIONr_mcangle_it4.9166.051544
X-RAY DIFFRACTIONr_mcangle_other4.9116.063545
X-RAY DIFFRACTIONr_scbond_it4.2614.813482
X-RAY DIFFRACTIONr_scbond_other4.2434.795480
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7966.94709
X-RAY DIFFRACTIONr_long_range_B_refined8.7332.5571034
X-RAY DIFFRACTIONr_long_range_B_other8.72832.5561034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 18 -
Rwork0.272 468 -
obs--99.39 %

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