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- PDB-7ups: Structural study of Legionella pneumophila effector DotY (Lpg0294) -

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Basic information

Entry
Database: PDB / ID: 7ups
TitleStructural study of Legionella pneumophila effector DotY (Lpg0294)
ComponentsDotY (Lpg0294)
KeywordsCELL INVASION / protein effector
Function / homology: / : / DotY / protein transport / cytoplasm / Type 4 apparatus protein DotY
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.43 Å
AuthorsChung, I.Y.W. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structural study of Legionella pneumophila effector DotY (Lpg0294), a component of the Dot/Icm type IV secretion system.
Authors: Chung, I.Y.W. / Cygler, M.
History
DepositionApr 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DotY (Lpg0294)
B: DotY (Lpg0294)
C: DotY (Lpg0294)
D: DotY (Lpg0294)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7608
Polymers95,5124
Non-polymers2484
Water3,495194
1
A: DotY (Lpg0294)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9402
Polymers23,8781
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DotY (Lpg0294)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9402
Polymers23,8781
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DotY (Lpg0294)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9402
Polymers23,8781
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DotY (Lpg0294)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9402
Polymers23,8781
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.200, 75.620, 101.200
Angle α, β, γ (deg.)90.000, 127.910, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 13 or (resid 14...
d_2ens_1(chain "B" and (resid 7 through 54 or (resid 55...
d_3ens_1(chain "C" and (resid 7 through 38 or (resid 39...
d_4ens_1(chain "D" and (resid 7 through 13 or (resid 14...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLNA3 - 70
d_12ens_1LYSGLYA84 - 188
d_13ens_1GLUILEA190 - 213
d_14ens_1SERSERA215
d_21ens_1ALAGLNB3 - 70
d_22ens_1LYSGLYB84 - 188
d_23ens_1GLUILEB190 - 213
d_24ens_1SERSERB215
d_31ens_1ALAGLYC3 - 175
d_32ens_1GLUILEC177 - 200
d_33ens_1SERSERC202
d_41ens_1ALAGLYD3 - 175
d_42ens_1GLUILED177 - 200
d_43ens_1SERSERD202

NCS oper:
IDCodeMatrixVector
1given(0.253041672934, 9.24228556323E-5, 0.96745537531), (-0.00259684045087, -0.999996328088, 0.000774745158716), (0.967451894503, -0.00270837006408, -0.25304050378)-2.32311614046, 29.4438571364, 2.96610293302
2given(-0.89360701926, 0.0954521936542, 0.438583371613), (-0.091518666555, -0.995346621884, 0.03015685622), (0.439421015429, -0.0131901869462, 0.898184385395)69.5789965479, 24.5330385047, -8.3929776138
3given(-0.204839657128, -0.00475969305721, -0.978783970133), (0.0852580827032, 0.99610058397, -0.0226866909754), (0.975075265916, -0.0880963786749, -0.203635099781)7.61834454722, -32.8965658846, 7.43948484654

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Components

#1: Protein
DotY (Lpg0294)


Mass: 23877.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0294 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q5ZYR7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsSNA at the amino-terminus is from the TEV protease cleavage site after removal of his-tag

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Citrate pH3.5, 25% PEG8k and 0.3M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.43→43.55 Å / Num. obs: 33201 / % possible obs: 95.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 43.64 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.35
Reflection shellResolution: 2.43→2.55 Å / Num. unique obs: 3535 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.43→43.54 Å / SU ML: 0.3741 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2622 989 2.98 %
Rwork0.2371 32187 -
obs0.2379 33176 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.27 Å2
Refinement stepCycle: LAST / Resolution: 2.43→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 16 194 6470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286370
X-RAY DIFFRACTIONf_angle_d0.56678576
X-RAY DIFFRACTIONf_chiral_restr0.0384977
X-RAY DIFFRACTIONf_plane_restr0.0041126
X-RAY DIFFRACTIONf_dihedral_angle_d15.7752374
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.361174744758
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS2.31172568165
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS2.38705046346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.560.36181070.3083665X-RAY DIFFRACTION77.23
2.56-2.720.32421420.30074534X-RAY DIFFRACTION95.1
2.72-2.930.37441440.28844758X-RAY DIFFRACTION99.96
2.93-3.220.28851510.25924768X-RAY DIFFRACTION99.86
3.22-3.690.25851460.23674772X-RAY DIFFRACTION99.74
3.69-4.650.21091450.20054809X-RAY DIFFRACTION99.8
4.65-43.540.23991540.22064881X-RAY DIFFRACTION99.74

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