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- PDB-5ysi: SdeA mART-C domain EE/AA NCA complex -

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Basic information

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


NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / host cell / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / nucleotidyltransferase activity ...NAD+-protein-arginine ADP-ribosyltransferase / deNEDDylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deneddylation / Transferases; Acyltransferases; Aminoacyltransferases / host cell / K63-linked deubiquitinase activity / protein deubiquitination / cysteine-type peptidase activity / nucleotidyltransferase activity / 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
NICOTINAMIDE / Ubiquitinating/deubiquitinating enzyme SdeA / SdeA
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.546 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

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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)17,0462
Polymers16,9241
Non-polymers1221
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint5 kcal/mol
Surface area8110 Å2
Unit cell
Length a, b, c (Å)37.867, 75.698, 84.682
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16923.611 Da / Num. of mol.: 1 / Fragment: UNP residues 761-960 / Mutation: E860A, E862A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: sdeA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q6RCR0, UniProt: Q5ZTK4*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Transferases; Acyltransferases; Aminoacyltransferases, NAD+-protein- ...References: UniProt: Q6RCR0, UniProt: Q5ZTK4*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Transferases; Acyltransferases; Aminoacyltransferases, NAD+-protein-arginine ADP-ribosyltransferase
#2: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.78 Å3/Da / Density % sol: 30.93 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
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: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.546→34.555 Å / Num. obs: 36284 / % possible obs: 99.56 % / Redundancy: 6.7 % / Net I/σ(I): 32.37
Reflection shellResolution: 1.546→1.602 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.542 / Num. unique obs: 1754 / % possible all: 97.33

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.546→34.555 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.65
RfactorNum. reflection% reflection
Rfree0.2458 3400 9.96 %
Rwork0.2038 --
obs0.208 34139 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.546→34.555 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 9 32 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111172
X-RAY DIFFRACTIONf_angle_d1.0911584
X-RAY DIFFRACTIONf_dihedral_angle_d14.995707
X-RAY DIFFRACTIONf_chiral_restr0.059181
X-RAY DIFFRACTIONf_plane_restr0.007205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5462-1.56830.32831370.26341227X-RAY DIFFRACTION93
1.5683-1.59170.30111360.26121240X-RAY DIFFRACTION99
1.5917-1.61660.27461490.26141317X-RAY DIFFRACTION100
1.6166-1.64310.31991410.25011308X-RAY DIFFRACTION99
1.6431-1.67140.34041370.26631241X-RAY DIFFRACTION100
1.6714-1.70180.25631450.24391320X-RAY DIFFRACTION100
1.7018-1.73460.25531360.2271251X-RAY DIFFRACTION100
1.7346-1.770.25971460.21961298X-RAY DIFFRACTION100
1.77-1.80850.28461440.21551281X-RAY DIFFRACTION100
1.8085-1.85050.24071430.20591303X-RAY DIFFRACTION100
1.8505-1.89680.26591390.19781299X-RAY DIFFRACTION100
1.8968-1.94810.24811370.20651263X-RAY DIFFRACTION100
1.9481-2.00540.27741460.21091302X-RAY DIFFRACTION99
2.0054-2.07010.23211410.21191276X-RAY DIFFRACTION100
2.0701-2.14410.2441420.2081287X-RAY DIFFRACTION100
2.1441-2.22990.31971460.20651304X-RAY DIFFRACTION99
2.2299-2.33140.24911400.21091249X-RAY DIFFRACTION99
2.3314-2.45430.22871410.19471273X-RAY DIFFRACTION100
2.4543-2.6080.28181410.19861286X-RAY DIFFRACTION99
2.608-2.80930.24031410.21111294X-RAY DIFFRACTION100
2.8093-3.09180.22111360.21891273X-RAY DIFFRACTION99
3.0918-3.53880.26181480.20521285X-RAY DIFFRACTION99
3.5388-4.45710.22321430.17081279X-RAY DIFFRACTION99
4.4571-34.56320.20661450.19251283X-RAY DIFFRACTION99

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