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- PDB-6geb: X-ray structure of the Legionella pneumophila ATPase DotB -

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Basic information

Entry
Database: PDB / ID: 6geb
TitleX-ray structure of the Legionella pneumophila ATPase DotB
ComponentsDotB
KeywordsHYDROLASE / AAA+ ATPase Type IVb secretion
Function / homologyDot/Icm secretion system ATPase DotB / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase / PHOSPHATE ION / DotB
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 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 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Oct 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 1.3Jan 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: DotB
B: DotB
C: DotB
D: DotB
E: DotB
F: DotB
G: DotB
H: DotB
I: DotB
J: DotB
K: DotB
L: DotB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,08724
Polymers529,94712
Non-polymers1,14012
Water0
1
A: DotB
B: DotB
C: DotB
D: DotB
E: DotB
F: DotB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,54312
Polymers264,9746
Non-polymers5706
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: DotB
H: DotB
I: DotB
J: DotB
K: DotB
L: DotB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,54312
Polymers264,9746
Non-polymers5706
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.200, 109.300, 119.800
Angle α, β, γ (deg.)83.700, 86.600, 60.700
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein
DotB / Type II secretory pathway / ATPase PulE/Tfp pilus assembly pathway / ATPase PilB


Mass: 44162.277 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria)
Gene: dotB, yggR, ERS240541_01758, ERS240560_02271, ERS253249_00407
Production host: Escherichia coli (E. coli) / References: UniProt: O52185
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4

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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: 2.5 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 1.2M of Na/K phosphate buffer pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.19→36.04 Å / Num. obs: 78104 / % possible obs: 98 % / Redundancy: 3.49 % / Net I/σ(I): 6.95
Reflection shellResolution: 3.19→3.31 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: 3.19→36.04 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.584
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 3841 4.9 %RANDOM
Rwork0.2331 ---
obs0.2345 78095 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 202.1 Å2 / Biso mean: 100.4151 Å2 / Biso min: 47.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20.5 Å20.36 Å2
2---0.63 Å2-0.42 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 3.19→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34602 0 60 0 34662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01935208
X-RAY DIFFRACTIONr_bond_other_d00.0233708
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.97847816
X-RAY DIFFRACTIONr_angle_other_deg3.578377920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91154406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30323.3891552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.383156234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.67615346
X-RAY DIFFRACTIONr_chiral_restr0.10.25688
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02138730
X-RAY DIFFRACTIONr_gen_planes_other0.0110.026936
X-RAY DIFFRACTIONr_mcbond_it3.7886.52417666
X-RAY DIFFRACTIONr_mcbond_other3.7886.52417665
X-RAY DIFFRACTIONr_mcangle_it6.1799.79222058
LS refinement shellResolution: 3.194→3.276 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 263 -
Rwork0.378 5209 -
all-5472 -
obs--93 %
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)
11.0918-0.39680.00763.30721.15960.59260.09850.08780.2377-0.1634-0.0510.1259-0.1345-0.1552-0.04750.2015-0.01080.03570.23950.16950.1789-53.363-33.3021.954
20.86961.17070.77981.6770.74171.9317-0.0109-0.01640.2012-0.0932-0.01030.2670.1466-0.11030.02120.10640.03520.05370.0980.10540.2377-33.553-4.7540.148
32.4409-0.59721.16570.7405-0.50631.76620.03660.02060.2341-0.02890.0744-0.1682-0.08850.2715-0.11090.1177-0.08480.05240.1375-0.05130.17012.3851.5113.738
40.756-0.3357-0.14412.3818-1.19651.0564-0.00350.0462-0.12250.1348-0.0612-0.25960.08620.06750.06470.209-0.0019-0.05540.16760.02820.154417.473-28.8643.276
52.27351.0199-1.02991.4798-0.45660.6987-0.10320.1098-0.4364-0.2690.0521-0.28560.2912-0.05320.05120.40130.0187-0.04640.16010.06980.26764.569-63.1175.382
62.7638-0.7728-0.14370.56220.37990.8501-0.02310.1903-0.2463-0.03520.03260.0871-0.0859-0.0369-0.00950.304-0.1290.00830.2060.07170.091-29.916-60.892.491
72.5311-1.3056-1.29121.59591.3121.6420.04950.259-0.3688-0.2598-0.0676-0.0490.1557-0.28640.01810.3867-0.11290.07290.31370.16670.3474-35.429-113.20764.014
81.08790.31810.14982.45150.99271.2568-0.0362-0.08040.03580.06040.10330.1123-0.1331-0.1902-0.0670.20980.04380.01850.23110.14620.1021-40.655-79.00462.808
92.75560.67460.9251.12220.08310.967-0.1275-0.09280.4098-0.10890.09250.0222-0.59130.25920.03510.7608-0.14120.12340.30050.01660.1856-18.7-50.11364.14
101.4722-0.89190.76160.5975-0.45341.08220.110.00150.1788-0.0596-0.0693-0.2024-0.38110.0482-0.04070.5048-0.29340.0530.42830.17890.235912.992-62.07761.408
110.70550.0822-0.36182.8668-1.13211.48860.05430.1256-0.0905-0.134-0.1662-0.13870.430.45960.11190.45530.02060.1020.5260.08380.311427.119-95.59162.831
122.62140.3227-0.17180.17-0.30130.8986-0.03470.2064-0.5242-0.06360.0748-0.00160.11590.0669-0.04020.6532-0.03160.15260.1560.01480.42650.725-117.22261.495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 372
2X-RAY DIFFRACTION2B4 - 374
3X-RAY DIFFRACTION3C5 - 373
4X-RAY DIFFRACTION4D6 - 373
5X-RAY DIFFRACTION5E6 - 372
6X-RAY DIFFRACTION6F5 - 373
7X-RAY DIFFRACTION7G4 - 372
8X-RAY DIFFRACTION8H4 - 374
9X-RAY DIFFRACTION9I5 - 373
10X-RAY DIFFRACTION10J6 - 373
11X-RAY DIFFRACTION11K6 - 372
12X-RAY DIFFRACTION12L5 - 373

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