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- PDB-7uyg: Structure of the first OTU domain from Legionella pneumophila eff... -

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Basic information

Entry
Database: PDB / ID: 7uyg
TitleStructure of the first OTU domain from Legionella pneumophila effector protein LotA
ComponentsLotA
KeywordsHYDROLASE / Deubiquitinase / OTU
Function / homologyIODIDE ION / Dot/Icm T4SS effector
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsPruneda, J.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142486 United States
CitationJournal: Mol.Cell / Year: 2023
Title: Mechanism of Lys6 poly-ubiquitin specificity by the L. pneumophila deubiquitinase LotA.
Authors: Warren, G.D. / Kitao, T. / Franklin, T.G. / Nguyen, J.V. / Geurink, P.P. / Kubori, T. / Nagai, H. / Pruneda, J.N.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LotA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,11010
Polymers34,0371
Non-polymers1,0739
Water5,152286
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)86.245, 86.245, 92.304
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 LotA


Mass: 34037.414 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 (E. coli) / References: UniProt: Q5ZTB4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG 2K MME, 0.2 M KI, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→39.07 Å / Num. obs: 56168 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.51 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 26.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2895 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.17.1_3660refinement
SHELXphasing
ARP/wARPmodel building
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→36.8 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 2895 5.15 %
Rwork0.1946 53273 -
obs0.196 56168 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 19 286 2447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582229
X-RAY DIFFRACTIONf_angle_d0.76923030
X-RAY DIFFRACTIONf_chiral_restr0.0463346
X-RAY DIFFRACTIONf_plane_restr0.0056393
X-RAY DIFFRACTIONf_dihedral_angle_d15.6932311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.29071230.25612521X-RAY DIFFRACTION99.96
1.52-1.550.26111420.24772460X-RAY DIFFRACTION100
1.55-1.580.2571190.22782542X-RAY DIFFRACTION100
1.58-1.610.23951440.21482496X-RAY DIFFRACTION99.96
1.61-1.640.22371400.20092473X-RAY DIFFRACTION100
1.64-1.680.25011400.20742509X-RAY DIFFRACTION100
1.68-1.720.22911370.20822510X-RAY DIFFRACTION99.96
1.72-1.760.24331480.20462509X-RAY DIFFRACTION100
1.76-1.810.24331550.20652482X-RAY DIFFRACTION99.96
1.81-1.860.21961570.20232490X-RAY DIFFRACTION99.85
1.86-1.920.24151290.20752538X-RAY DIFFRACTION99.96
1.92-1.990.20231110.19982531X-RAY DIFFRACTION100
1.99-2.070.23231370.19862545X-RAY DIFFRACTION100
2.07-2.160.20731610.19372510X-RAY DIFFRACTION100
2.16-2.280.24551340.19382531X-RAY DIFFRACTION99.89
2.28-2.420.21321370.19322547X-RAY DIFFRACTION99.96
2.42-2.610.23351110.19962593X-RAY DIFFRACTION99.96
2.61-2.870.2241070.19832602X-RAY DIFFRACTION99.96
2.87-3.280.221290.20022589X-RAY DIFFRACTION99.96
3.28-4.140.19881660.17092581X-RAY DIFFRACTION99.17
4.14-36.80.21781680.19022714X-RAY DIFFRACTION98.73
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)
13.432331800980.571877602631-0.9050236259012.317100124750.2134915460812.07347153208-0.0733990310321-0.1473265647880.1640694450770.198662392081-0.130675053326-0.347297007776-0.4485584306630.2822509999530.1348791214880.239668234656-0.0522190369247-0.06397342951920.1614174405450.03868256273260.2076740492613.845934693-9.5591512036652.7749167952
21.81685338514-0.0514529543682-0.674269456172.11906344227-0.3616394915432.548409997540.0288340449199-0.153306419094-0.04201107537570.0219407024536-0.0182915975057-0.02952435053340.04696907382710.0751458298997-0.009219765644460.0875208017107-0.0153270220059-0.008073793734760.1361182294660.002315142833120.11842525943341.2600435247.8037371028868.2162332019
34.37385567156-0.110380269487-0.6273734596382.18085840952-0.6782097469272.2371017822-0.0410545622165-0.01192607268920.650074909153-0.00871539262241-0.173215615093-0.502342496544-0.7999354243630.349257498980.1472715303530.455577784384-0.0817490098361-0.0627237609810.2887062649280.05109023005290.42413752100516.7450281894-3.3642557669547.182282573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 275 )

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