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- PDB-5ysj: SdeA mART-C domain WT apo -

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Basic information

Entry
Database: PDB / ID: 5ysj
TitleSdeA mART-C domain WT apo
ComponentsUbiquitinating/deubiquitinating enzyme SdeA
KeywordsHYDROLASE / E3 ligase
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 / nucleotidyltransferase activity / cysteine-type peptidase 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 / 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: 2.059 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 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
B: Ubiquitinating/deubiquitinating enzyme SdeA
C: Ubiquitinating/deubiquitinating enzyme SdeA
D: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)67,5964
Polymers67,5964
Non-polymers00
Water1,06359
1
A: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,8991
Polymers16,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,8991
Polymers16,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,8991
Polymers16,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitinating/deubiquitinating enzyme SdeA


Theoretical massNumber of molelcules
Total (without water)16,8991
Polymers16,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.962, 86.682, 71.027
Angle α, β, γ (deg.)90.00, 97.90, 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: 16898.998 Da / Num. of mol.: 4
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.: 59 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
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: Sep 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.059→43.54 Å / Num. obs: 32455 / % possible obs: 99.01 % / Redundancy: 4 % / Net I/σ(I): 16.53

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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: 2.059→43.54 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2694 1996 6.16 %
Rwork0.2254 --
obs0.2281 32401 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.059→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4417 0 0 59 4476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034497
X-RAY DIFFRACTIONf_angle_d0.7256079
X-RAY DIFFRACTIONf_dihedral_angle_d14.3542747
X-RAY DIFFRACTIONf_chiral_restr0.044706
X-RAY DIFFRACTIONf_plane_restr0.003780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0589-2.11040.33481290.2991952X-RAY DIFFRACTION89
2.1104-2.16740.30261430.28392168X-RAY DIFFRACTION100
2.1674-2.23120.33931420.27062172X-RAY DIFFRACTION100
2.2312-2.30320.32671410.26752152X-RAY DIFFRACTION98
2.3032-2.38550.28851430.25532195X-RAY DIFFRACTION100
2.3855-2.4810.281440.23982174X-RAY DIFFRACTION100
2.481-2.59390.31471440.23652193X-RAY DIFFRACTION100
2.5939-2.73070.26591430.24112184X-RAY DIFFRACTION100
2.7307-2.90170.26911440.23632191X-RAY DIFFRACTION100
2.9017-3.12570.28251450.22172202X-RAY DIFFRACTION100
3.1257-3.44010.2561430.22882193X-RAY DIFFRACTION100
3.4401-3.93770.27951440.2082185X-RAY DIFFRACTION100
3.9377-4.95990.22751440.17592208X-RAY DIFFRACTION100
4.9599-43.55430.23151470.21822236X-RAY DIFFRACTION99

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