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- PDB-6yk8: OTU-like deubiquitinase from Legionella -Lpg2529 -

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Basic information

Entry
Database: PDB / ID: 6yk8
TitleOTU-like deubiquitinase from Legionella -Lpg2529
ComponentsUncharacterized protein
KeywordsCELL INVASION / deubiquitinase / legionella / OTU / effector protein
Function / homology: / Dot/Icm T4SS effector
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.42 Å
AuthorsShin, D. / Dikic, I.
CitationJournal: Elife / Year: 2020
Title: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection.
Authors: Shin, D. / Bhattacharya, A. / Cheng, Y.L. / Alonso, M.C. / Mehdipour, A.R. / van der Heden van Noort, G.J. / Ovaa, H. / Hummer, G. / Dikic, I.
History
DepositionApr 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,45512
Polymers69,5042
Non-polymers1,95110
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-183 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.534, 140.979, 57.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Uncharacterized protein


Mass: 34752.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSI8
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % PEG3350, 100 mM Tris-HCl pH 8.5, 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.070333 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.070333 Å / Relative weight: 1
ReflectionResolution: 2.42→44.53 Å / Num. obs: 23185 / % possible obs: 99.23 % / Redundancy: 2 % / Biso Wilson estimate: 61.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03065 / Net I/σ(I): 14.85
Reflection shellResolution: 2.42→2.506 Å / Rmerge(I) obs: 0.3765 / Num. unique obs: 2278 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: SAD / Resolution: 2.42→44.53 Å / SU ML: 0.4094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9252
RfactorNum. reflection% reflection
Rfree0.2831 1109 4.79 %
Rwork0.2285 --
obs0.2312 23154 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 76.55 Å2
Refinement stepCycle: LAST / Resolution: 2.42→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 10 1 4383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00854464
X-RAY DIFFRACTIONf_angle_d0.99356041
X-RAY DIFFRACTIONf_chiral_restr0.0547683
X-RAY DIFFRACTIONf_plane_restr0.0064779
X-RAY DIFFRACTIONf_dihedral_angle_d21.7505588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.530.42351040.32582779X-RAY DIFFRACTION99.48
2.53-2.660.36481500.29482719X-RAY DIFFRACTION99.55
2.66-2.830.37891530.28522727X-RAY DIFFRACTION99.52
2.83-3.050.35421600.27412734X-RAY DIFFRACTION98.67
3.05-3.360.32991410.26252759X-RAY DIFFRACTION99.76
3.36-3.840.33031460.24292803X-RAY DIFFRACTION99.46
3.84-4.840.24541260.19922742X-RAY DIFFRACTION98.83
4.84-44.530.22311290.19982782X-RAY DIFFRACTION98.71

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