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- PDB-6g0c: Crystal structure of SdeA catalytic core -

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Basic information

Entry
Database: PDB / ID: 6g0c
TitleCrystal structure of SdeA catalytic core
ComponentsUbiquitinating/deubiquitinating enzyme SdeA
KeywordsHYDROLASE / ubiquitination SdeA
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / nucleotidyltransferase activity / host cell ...NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / nucleotidyltransferase activity / host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein ubiquitination / nucleotide binding / proteolysis / extracellular region
Similarity search - Function
SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Ubiquitinating/deubiquitinating enzyme SdeA
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsKalayil, S. / Bhogaraju, S. / Basquin, J. / Dikic, I.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationSFB 1177 Germany
ERC742720 Germany
German Research FoundationSPP 1580 Germany
CitationJournal: Nature / Year: 2018
Title: Insights into catalysis and function of phosphoribosyl-linked serine ubiquitination.
Authors: Kalayil, S. / Bhogaraju, S. / Bonn, F. / Shin, D. / Liu, Y. / Gan, N. / Basquin, J. / Grumati, P. / Luo, Z.Q. / Dikic, I.
History
DepositionMar 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Ubiquitinating/deubiquitinating enzyme SdeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3665
Polymers78,9791
Non-polymers3874
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint12 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.721, 80.824, 86.518
Angle α, β, γ (deg.)90.00, 110.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitinating/deubiquitinating enzyme SdeA / Effector protein SdeA


Mass: 78978.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: sdeA, lpg2157 / Plasmid: pET21 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q5ZTK4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Transferases; Acyltransferases; Aminoacyltransferases, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2

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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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7
Details: 100mM Bis Tris Propane pH 7.0-8.0, 0.1-0.2M sodium citrate tribasic dihydrate, 20-30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.802→44.216 Å / Num. obs: 43693 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 13.03
Reflection shellResolution: 2.802→2.902 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: It was solved by MR on a crude model from experimental phasing experiment (data not deposited)

Resolution: 2.802→44.216 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 35.61
RfactorNum. reflection% reflection
Rfree0.2932 2199 5.03 %
Rwork0.2578 --
obs0.2597 43693 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.802→44.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 25 0 4863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034957
X-RAY DIFFRACTIONf_angle_d0.5056717
X-RAY DIFFRACTIONf_dihedral_angle_d14.5182958
X-RAY DIFFRACTIONf_chiral_restr0.038751
X-RAY DIFFRACTIONf_plane_restr0.003880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8018-2.86270.41551270.45712351X-RAY DIFFRACTION92
2.8627-2.92930.38631380.40562610X-RAY DIFFRACTION100
2.9293-3.00250.3861410.38492618X-RAY DIFFRACTION99
3.0025-3.08370.38221410.36222639X-RAY DIFFRACTION100
3.0837-3.17440.35191360.35772581X-RAY DIFFRACTION100
3.1744-3.27690.40751360.33952619X-RAY DIFFRACTION100
3.2769-3.39390.34721380.30232634X-RAY DIFFRACTION100
3.3939-3.52980.33991340.28522596X-RAY DIFFRACTION100
3.5298-3.69030.34721410.28562623X-RAY DIFFRACTION100
3.6903-3.88480.30241370.2622579X-RAY DIFFRACTION100
3.8848-4.1280.2761390.24192626X-RAY DIFFRACTION100
4.128-4.44650.26961360.22262591X-RAY DIFFRACTION100
4.4465-4.89340.22471370.20152604X-RAY DIFFRACTION100
4.8934-5.60030.24151390.21532621X-RAY DIFFRACTION100
5.6003-7.05120.31561410.23992618X-RAY DIFFRACTION100
7.0512-44.22170.22461380.19622584X-RAY DIFFRACTION99
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)
11.92430.1906-0.81223.0586-0.45044.1816-0.1068-0.0299-0.0732-0.24870.0102-0.27030.40070.15520.07210.5986-0.0356-0.11050.3132-0.04550.5004-35.8783-42.42994.3208
23.6650.73511.28396.15791.22254.8527-0.13180.3287-0.4097-0.5817-0.22150.56430.5368-0.80950.29590.5696-0.1304-0.02770.5513-0.07730.4698-55.7819-44.29133.662
32.28270.36090.12223.61120.13032.6525-0.00230.0861-0.0235-0.1517-0.19080.61330.1589-0.64960.19560.61910.0575-0.11750.6439-0.0520.496-58.1865-42.9564-1.31
42.1024-1.48620.3071.0557-0.25010.4342-0.25610.2380.1033-0.27680.2340.2443-0.41380.0414-0.00741.39790.0009-0.32781.01850.03370.7397-74.0043-2.743116.9704
55.36280.96491.93445.65820.34236.6198-0.20640.37010.51380.1587-0.1107-0.5163-0.85890.63790.30690.8462-0.0747-0.15580.69140.12360.4948-66.15398.838524.6663
63.56231.6541.1665.48942.36924.8271-0.3558-0.62110.20760.3810.1563-0.2053-0.1448-0.46470.10080.8470.1434-0.04660.7199-0.02910.5139-48.6005-38.060130.9949
71.03160.5392.38542.59983.14097.2316-1.10950.39180.3153-0.23090.43050.2903-0.34450.47730.78461.10940.1009-0.22750.7764-0.01680.5588-42.8811-26.482835.226
88.55831.21654.86085.96691.36375.6647-0.575-0.75430.96130.63340.2631-0.0056-0.557-0.27890.36511.01190.1182-0.14550.6923-0.07260.4634-45.6291-31.37434.126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 222:413)
2X-RAY DIFFRACTION2(chain A and resid 414:465)
3X-RAY DIFFRACTION3(chain A and resid 466:582)
4X-RAY DIFFRACTION4(chain A and resid 583:632)
5X-RAY DIFFRACTION5(chain A and resid 633:756)
6X-RAY DIFFRACTION6(chain A and resid 757:795)
7X-RAY DIFFRACTION7(chain A and resid 796:829)
8X-RAY DIFFRACTION8(chain A and resid 830:901)

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