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- PDB-6g7c: Nt2-CTD domains of the TssA component from the type VI secretion ... -

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Basic information

Entry
Database: PDB / ID: 6g7c
TitleNt2-CTD domains 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 / MOLECULAR REPLACEMENT / Resolution: 3.13 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

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Assembly

Deposited unit
A: ImpA-related domain protein
B: ImpA-related domain protein
G: ImpA-related domain protein
H: ImpA-related domain protein
C: ImpA-related domain protein
D: ImpA-related domain protein
I: ImpA-related domain protein
J: ImpA-related domain protein
E: ImpA-related domain protein
F: ImpA-related domain protein


Theoretical massNumber of molelcules
Total (without water)295,90410
Polymers295,90410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24410 Å2
ΔGint-163 kcal/mol
Surface area114020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.034, 202.076, 139.013
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ImpA-related domain protein


Mass: 29590.373 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag (MGSSHHHHHHSGAP)
Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila ATCC 7966 (bacteria)
Gene: AHA_1844 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0KJC7

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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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate, 0.1 M sodium citrate (pH 5.5), and 10 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 3.13→202.08 Å / Num. obs: 67977 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.077 / Net I/σ(I): 5.8
Reflection shellResolution: 3.13→3.21 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→202.08 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.859 / SU B: 42.338 / SU ML: 0.642 / Cross valid method: THROUGHOUT / ESU R Free: 0.557 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32758 3380 5 %RANDOM
Rwork0.25511 ---
obs0.25856 64474 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 97.066 Å2
Baniso -1Baniso -2Baniso -3
1-8.18 Å20 Å2-5.04 Å2
2---5.11 Å20 Å2
3----2.94 Å2
Refinement stepCycle: 1 / Resolution: 3.13→202.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18363 0 0 0 18363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01918764
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217450
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.95325443
X-RAY DIFFRACTIONr_angle_other_deg0.905340222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.31652322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49823.34931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.876153087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.99315190
X-RAY DIFFRACTIONr_chiral_restr0.0910.22734
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02121179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023991
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_it6.6189.7749348
X-RAY DIFFRACTIONr_mcbond_other6.6189.7749347
X-RAY DIFFRACTIONr_mcangle_it10.72414.64811650
X-RAY DIFFRACTIONr_mcangle_other10.72314.64811651
X-RAY DIFFRACTIONr_scbond_it5.64310.0479416
X-RAY DIFFRACTIONr_scbond_other5.64310.0479417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.64614.93113794
X-RAY DIFFRACTIONr_long_range_B_refined14.77722023
X-RAY DIFFRACTIONr_long_range_B_other14.77722024
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.13→3.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 251 -
Rwork0.447 4754 -
obs--99.54 %

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