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- PDB-6gef: X-ray structure of the Yersinia pseudotuberculosis ATPase DotB -

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Basic information

Entry
Database: PDB / ID: 6gef
TitleX-ray structure of the Yersinia pseudotuberculosis ATPase DotB
ComponentsType IV secretion system protein DotB
KeywordsHYDROLASE / AAA+ ATPase Type IVb secretion
Function / homologyType II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase / Type IV secretion system protein DotB
Function and homology information
Biological speciesYersinia pseudotuberculosis IP 31758 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPrevost, M.S. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council321630 United Kingdom
CitationJournal: Protein Sci. / Year: 2018
Title: X-ray crystal structures of the type IVb secretion system DotB ATPases.
Authors: Prevost, M.S. / Waksman, G.
History
DepositionApr 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Type IV secretion system protein DotB
B: Type IV secretion system protein DotB
C: Type IV secretion system protein DotB
D: Type IV secretion system protein DotB
E: Type IV secretion system protein DotB
F: Type IV secretion system protein DotB


Theoretical massNumber of molelcules
Total (without water)270,1886
Polymers270,1886
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20840 Å2
ΔGint-38 kcal/mol
Surface area91560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.040, 93.560, 109.920
Angle α, β, γ (deg.)103.900, 101.980, 99.940
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Type IV secretion system protein DotB


Mass: 45031.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis IP 31758 (bacteria)
Gene: YpsIP31758_B0110 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1QTI9

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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 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na/Cacodylate buffer pH5.5 and 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.75→40.57 Å / Num. obs: 77292 / % possible obs: 97.8 % / Redundancy: 3.49 % / Net I/σ(I): 10.33
Reflection shellResolution: 2.75→2.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EWV, 5FL3

2ewv

5fl3


Resolution: 2.75→40.56 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.628 / ESU R Free: 0.414
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2962 3866 5 %RANDOM
Rwork0.2546 ---
obs0.2567 77292 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.55 Å2 / Biso mean: 76.0573 Å2 / Biso min: 37.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å2-0.19 Å20.4 Å2
2---1.39 Å22.57 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18021 0 0 0 18021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01918348
X-RAY DIFFRACTIONr_bond_other_d00.0217236
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.95924837
X-RAY DIFFRACTIONr_angle_other_deg3.622339940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.25752307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97423.693807
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.779153233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.38515136
X-RAY DIFFRACTIONr_chiral_restr0.0710.22892
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120317
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023691
X-RAY DIFFRACTIONr_mcbond_it2.9414.2569246
X-RAY DIFFRACTIONr_mcbond_other2.9414.2559245
X-RAY DIFFRACTIONr_mcangle_it4.6336.3911547
LS refinement shellResolution: 2.754→2.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 261 -
Rwork0.427 5017 -
all-5278 -
obs--91.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.28070.5194-0.19911.3924-0.97991.43020.0278-0.1721-0.00370.1888-0.239-0.1132-0.00870.24910.21120.2245-0.0280.04940.3281-0.12220.129-3.696-0.4166.052
22.90490.10470.86211.4644-0.43961.00510.0828-0.1582-0.1085-0.11230.02880.14790.3865-0.1322-0.11160.4214-0.03220.04160.31-0.130.1197-26.247-25.684-5.897
32.25360.24490.5241.2094-0.56551.08420.15590.0227-0.0057-0.1349-0.04310.14570.1742-0.085-0.11270.4206-0.04330.05790.193-0.1260.1206-43.823-21.235-34.745
41.081.03250.37072.1362-0.23041.4518-0.0060.07580.48590.02780.00020.4718-0.149-0.14430.00590.30080.02220.05230.3341-0.07650.318-48.5817.318-57.231
50.6370.63660.60781.81311.00281.9558-0.06830.10630.1728-0.11930.00550.1813-0.12280.03150.06280.24130.03010.06640.2456-0.11060.1972-21.94830.111-48.556
60.91790.25060.30741.7364-0.05332.42260.0156-0.1157-0.00040.084-0.1896-0.17540.00710.20120.1740.1146-0.02760.04770.2353-0.090.128-1.86824.115-21.701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 388
2X-RAY DIFFRACTION2B5 - 388
3X-RAY DIFFRACTION3C4 - 388
4X-RAY DIFFRACTION4D3 - 387
5X-RAY DIFFRACTION5E3 - 387
6X-RAY DIFFRACTION6F3 - 388

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