[English] 日本語
Yorodumi
- PDB-5ysk: SdeA mART-C domain EE/AA apo -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 2.403 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG400, Tris

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more