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- PDB-7f9x: Structure of the second OTU domain of LotA -

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Basic information

Entry
Database: PDB / ID: 7f9x
TitleStructure of the second OTU domain of LotA
ComponentsLotA
KeywordsHYDROLASE / Legionella effector / deubiquitinase
Function / homologyDot/Icm T4SS effector
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsIwai, T. / Takekawa, T. / Kubori, T. / Nagai, H. / Imada, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H03469 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03470 Japan
CitationJournal: J.Bacteriol. / Year: 2022
Title: Structural Basis of Ubiquitin Recognition by a Bacterial Ovarian Tumor Deubiquitinase LotA.
Authors: Takekawa, N. / Kubori, T. / Iwai, T. / Nagai, H. / Imada, K.
History
DepositionJul 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LotA


Theoretical massNumber of molelcules
Total (without water)28,9461
Polymers28,9461
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13490 Å2
Unit cell
Length a, b, c (Å)77.150, 94.120, 83.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21A-695-

HOH

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Components

#1: Protein LotA


Mass: 28945.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2248 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZTB4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 39% (w/v) PEG200, 0.1 M NaOAc pH4.5 and 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.97→83.79 Å / Num. obs: 21904 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 19.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.042 / Net I/σ(I): 11.1
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1502 / CC1/2: 0.833 / Rpim(I) all: 0.25 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→83.79 Å / SU ML: 0.2228 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2276 1080 4.93 %
Rwork0.1933 20818 -
obs0.195 21898 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.86 Å2
Refinement stepCycle: LAST / Resolution: 1.97→83.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 170 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842011
X-RAY DIFFRACTIONf_angle_d1.01842739
X-RAY DIFFRACTIONf_chiral_restr0.056305
X-RAY DIFFRACTIONf_plane_restr0.0055363
X-RAY DIFFRACTIONf_dihedral_angle_d22.6526265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.060.33341350.24322551X-RAY DIFFRACTION99.93
2.06-2.170.25261120.21622592X-RAY DIFFRACTION99.89
2.17-2.30.25621400.19332558X-RAY DIFFRACTION99.93
2.3-2.480.23871600.1862554X-RAY DIFFRACTION99.56
2.48-2.730.251120.18132600X-RAY DIFFRACTION99.63
2.73-3.130.22831160.1832633X-RAY DIFFRACTION99.78
3.13-3.940.21441500.17312615X-RAY DIFFRACTION100
3.94-83.790.19321550.20462715X-RAY DIFFRACTION99.41

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