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- PDB-5ysk: SdeA mART-C domain EE/AA apo -

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Basic information

Entry
Database: PDB / ID: 5ysk
TitleSdeA mART-C domain EE/AA apo
ComponentsUbiquitinating/deubiquitinating enzyme SdeA
KeywordsHYDROLASE / E3 ligase
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / deNEDDylase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / nucleotidyltransferase activity / cysteine-type peptidase activity / host cell ...NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / deNEDDylase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / K63-linked deubiquitinase activity / protein deubiquitination / nucleotidyltransferase activity / cysteine-type peptidase 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
Ubiquitinating/deubiquitinating enzyme SdeA
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsKim, L. / Kwon, D.H. / Song, H.K.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila
Authors: Kim, L. / Kwon, D.H. / Kim, B.H. / Kim, J. / Park, M.R. / Park, Z.Y. / Song, H.K.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitinating/deubiquitinating enzyme SdeA
B: Ubiquitinating/deubiquitinating enzyme SdeA
C: Ubiquitinating/deubiquitinating enzyme SdeA
D: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)67,6944
Polymers67,6944
Non-polymers00
Water2,144119
1
A: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,9241
Polymers16,9241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,9241
Polymers16,9241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,9241
Polymers16,9241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,9241
Polymers16,9241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.750, 85.360, 70.795
Angle α, β, γ (deg.)90.00, 97.11, 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: 16923.611 Da / Num. of mol.: 4 / Mutation: E860A, E862A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: sdeA, lpg2157 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5ZTK4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400, Tris

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.403→32.42 Å / Num. obs: 19830 / % possible obs: 97.99 % / Redundancy: 3.6 % / Net I/σ(I): 34.6762

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.403→32.42 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 28.14
RfactorNum. reflection% reflection
Rfree0.2614 1980 10 %
Rwork0.1852 --
obs0.1926 19805 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.403→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 0 119 4427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134386
X-RAY DIFFRACTIONf_angle_d1.2135932
X-RAY DIFFRACTIONf_dihedral_angle_d16.0792677
X-RAY DIFFRACTIONf_chiral_restr0.061696
X-RAY DIFFRACTIONf_plane_restr0.007756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4033-2.46330.31071200.18691083X-RAY DIFFRACTION84
2.4633-2.52990.2811430.17661288X-RAY DIFFRACTION99
2.5299-2.60440.27091430.17691276X-RAY DIFFRACTION99
2.6044-2.68840.27951410.19381272X-RAY DIFFRACTION100
2.6884-2.78450.27151440.18091296X-RAY DIFFRACTION99
2.7845-2.89590.2771430.18781295X-RAY DIFFRACTION100
2.8959-3.02770.26241420.18031274X-RAY DIFFRACTION100
3.0277-3.18720.32071430.18571299X-RAY DIFFRACTION100
3.1872-3.38680.25271440.17891295X-RAY DIFFRACTION100
3.3868-3.64810.26041450.18461300X-RAY DIFFRACTION100
3.6481-4.01490.21981430.17361288X-RAY DIFFRACTION100
4.0149-4.59510.21181420.1521281X-RAY DIFFRACTION99
4.5951-5.78640.2631450.19391304X-RAY DIFFRACTION99
5.7864-39.16660.28751420.24951274X-RAY DIFFRACTION95

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