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- PDB-6g7b: Nt2 domain of the TssA component from the type VI secretion syste... -

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Basic information

Entry
Database: PDB / ID: 6g7b
TitleNt2 domain of the TssA component from the type VI secretion system of Aeromonas hydrophila.
ComponentsImpA-related domain protein
KeywordsTRANSPORT PROTEIN / Type VI secretion system component / alpha helical protein / TssA / Aeromonas hydrophila
Function / homologyType VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / ImpA-related domain protein
Function and homology information
Biological speciesAeromonas hydrophila subsp. hydrophila ATCC 7966 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsDix, S.D. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Tzokov, S.B. ...Dix, S.D. / Owen, H.J. / Sun, R. / Ahmad, A. / Shastri, S. / Spiewak, H.L. / Mosby, D.J. / Harris, M.J. / Batters, S.L. / Tzokov, S.B. / Sedelnikova, S.E. / Baker, P.J. / Bullough, P.A. / Rice, D.W. / Thomas, M.S.
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
DepositionApr 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 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

Downloads & links

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Assembly

Deposited unit
D: ImpA-related domain protein
B: ImpA-related domain protein
A: ImpA-related domain protein
C: ImpA-related domain protein


Theoretical massNumber of molelcules
Total (without water)166,5464
Polymers166,5464
Non-polymers00
Water6,846380
1
D: ImpA-related domain protein
C: ImpA-related domain protein


Theoretical massNumber of molelcules
Total (without water)83,2732
Polymers83,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area14850 Å2
MethodPISA
2
B: ImpA-related domain protein
A: ImpA-related domain protein


Theoretical massNumber of molelcules
Total (without water)83,2732
Polymers83,2732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-9 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.848, 101.316, 78.432
Angle α, β, γ (deg.)90.00, 104.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ImpA-related domain protein


Mass: 41636.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag (LEHHHHHH)
Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila ATCC 7966 (bacteria)
Gene: AHA_1844 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0KJC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 0.2 M Sodium chloride, 0.1 M HEPES buffer (pH 7.0), and 20% (w/v) PEG 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.76→101.32 Å / Num. obs: 59629 / % possible obs: 99.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.039 / Net I/σ(I): 7
Reflection shellResolution: 1.76→1.79 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→101.32 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.904 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30575 2805 4.7 %RANDOM
Rwork0.27227 ---
obs0.27382 56717 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.03 Å2
2---1.24 Å20 Å2
3---1.81 Å2
Refinement stepCycle: 1 / Resolution: 1.76→101.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 0 380 4964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194696
X-RAY DIFFRACTIONr_bond_other_d0.0010.024384
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9586380
X-RAY DIFFRACTIONr_angle_other_deg1.025310108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78422.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92915760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0111548
X-RAY DIFFRACTIONr_chiral_restr0.0990.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021020
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_it1.8012.0812332
X-RAY DIFFRACTIONr_mcbond_other1.8012.082331
X-RAY DIFFRACTIONr_mcangle_it2.593.1062908
X-RAY DIFFRACTIONr_mcangle_other2.5893.1072909
X-RAY DIFFRACTIONr_scbond_it2.8482.4072364
X-RAY DIFFRACTIONr_scbond_other2.8482.4062362
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3483.4883472
X-RAY DIFFRACTIONr_long_range_B_refined5.58925.3185571
X-RAY DIFFRACTIONr_long_range_B_other5.50125.0715485
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 198 -
Rwork0.467 4185 -
obs--98.85 %

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