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- PDB-6hs5: N-terminal domain including the conserved ImpA_N region of the Ts... -

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Basic information

Entry
Database: PDB / ID: 6hs5
TitleN-terminal domain including the conserved ImpA_N region 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 / SAD / Resolution: 1.8 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
DepositionSep 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TssA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9574
Polymers30,8151
Non-polymers1423
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-8 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.670, 125.740, 45.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

CA

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Components

#1: Protein TssA


Mass: 30815.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag followed by a thrombin cleavage site - MGSSHHHHHHSSGLVPRGSH Construct comprises residues 1-255 of full-length protein (total 373 residues)
Source: (gene. exp.) Burkholderia cenocepacia H111 (bacteria)
Gene: I35_RS01755 / Plasmid: pET14b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1V2W6E8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.16M calcium acetate, 0.08M sodium cacodylate pH6.5, 14.4% (w/v) PEG8000, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.04434 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04434 Å / Relative weight: 1
ReflectionResolution: 1.8→49.67 Å / Num. obs: 27244 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.022 / Net I/σ(I): 21.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1966 / CC1/2: 0.909 / Rpim(I) all: 0.177 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→46.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.567 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22594 1381 5.1 %RANDOM
Rwork0.17719 ---
obs0.17966 25817 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.33 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 6 119 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192041
X-RAY DIFFRACTIONr_bond_other_d0.0020.021890
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9532774
X-RAY DIFFRACTIONr_angle_other_deg1.00734337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3223.394109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09115324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6391521
X-RAY DIFFRACTIONr_chiral_restr0.1030.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
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_it34.9912.3611000
X-RAY DIFFRACTIONr_mcbond_other35.0012.357999
X-RAY DIFFRACTIONr_mcangle_it25.9023.4171248
X-RAY DIFFRACTIONr_mcangle_other25.8933.4181249
X-RAY DIFFRACTIONr_scbond_it53.9013.4561041
X-RAY DIFFRACTIONr_scbond_other53.8993.4571041
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other36.6984.471524
X-RAY DIFFRACTIONr_long_range_B_refined38.50920.6642491
X-RAY DIFFRACTIONr_long_range_B_other38.95720.4882432
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 96 -
Rwork0.235 1861 -
obs--98.84 %

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