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- PDB-8gok: Legionella OTU deubiquitinase LotA OTU1 domain -

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Basic information

Entry
Database: PDB / ID: 8gok
TitleLegionella OTU deubiquitinase LotA OTU1 domain
ComponentsLegionella OTU-deubiquitinase A OTU1 domain
KeywordsHYDROLASE / Deubiquitinase / Ubiquitin / Legionella
Function / homologyDot/Icm T4SS effector
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsShin, D. / Kang, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1C1C100396112 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A6A1A0302560722 Korea, Republic Of
CitationJournal: To Be Published
Title: Legionella OTU deubiquitinase LotA OTU1 domain
Authors: Shin, D. / Kang, S.
History
DepositionAug 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Legionella OTU-deubiquitinase A OTU1 domain


Theoretical massNumber of molelcules
Total (without water)31,3601
Polymers31,3601
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.217, 86.217, 91.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Legionella OTU-deubiquitinase A OTU1 domain


Mass: 31360.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2248 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZTB4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 35% (w/v) PEG 4000, 0.1M Tris-HCl [pH7.8], 0.8 M Lithium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.52→40.48 Å / Num. obs: 53716 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 20.69 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01733 / Rpim(I) all: 0.01733 / Rrim(I) all: 0.0245 / Net I/σ(I): 18.91
Reflection shellResolution: 1.52→1.574 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4571 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 5296 / CC1/2: 0.641 / CC star: 0.884 / Rpim(I) all: 0.4571 / Rrim(I) all: 0.6464 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F9X

7f9x


Resolution: 1.52→40.48 Å / SU ML: 0.1827 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 2585 4.81 %
Rwork0.1951 51122 -
obs0.196 53707 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.43 Å2
Refinement stepCycle: LAST / Resolution: 1.52→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 0 323 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642282
X-RAY DIFFRACTIONf_angle_d0.90513093
X-RAY DIFFRACTIONf_chiral_restr0.0549342
X-RAY DIFFRACTIONf_plane_restr0.0075406
X-RAY DIFFRACTIONf_dihedral_angle_d5.3999304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.550.32391390.29692799X-RAY DIFFRACTION99.9
1.55-1.580.30441680.28512769X-RAY DIFFRACTION100
1.58-1.620.31251300.25732796X-RAY DIFFRACTION100
1.62-1.650.28881510.24142810X-RAY DIFFRACTION100
1.65-1.690.25681620.23292786X-RAY DIFFRACTION99.97
1.69-1.740.22251580.21482763X-RAY DIFFRACTION100
1.74-1.790.22921390.21242805X-RAY DIFFRACTION99.93
1.79-1.850.26431290.21432822X-RAY DIFFRACTION99.97
1.85-1.920.25011180.21412851X-RAY DIFFRACTION100
1.92-1.990.20331390.20212811X-RAY DIFFRACTION100
1.99-2.080.22691500.1992808X-RAY DIFFRACTION99.97
2.08-2.190.221500.1882824X-RAY DIFFRACTION100
2.19-2.330.23121320.20012870X-RAY DIFFRACTION100
2.33-2.510.22311380.19032850X-RAY DIFFRACTION99.97
2.51-2.760.20671600.19732843X-RAY DIFFRACTION99.97
2.76-3.160.21491110.19812928X-RAY DIFFRACTION100
3.16-3.980.18681540.17292904X-RAY DIFFRACTION100
3.98-40.480.18381570.17743083X-RAY DIFFRACTION99.88

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