[English] 日本語
Yorodumi
- PDB-5zq2: SidE apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zq2
TitleSidE apo form
ComponentsSidE
KeywordsCELL INVASION / ubiquitination
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity / protein deubiquitination / nucleotide binding
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
Uncharacterized protein laiD / SidE
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsWang, Y. / Gao, A. / Gao, P.
Funding support China, 4items
OrganizationGrant numberCountry
Other government91753133 China
Other government31670903 China
Other government31700687 China
Other governmentXDB08020204 China
CitationJournal: Cell / Year: 2018
Title: Structural Insights into Non-canonical Ubiquitination Catalyzed by SidE.
Authors: Wang, Y. / Shi, M. / Feng, H. / Zhu, Y. / Liu, S. / Gao, A. / Gao, P.
History
DepositionApr 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 14, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SidE
C: SidE


Theoretical massNumber of molelcules
Total (without water)192,0322
Polymers192,0322
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-33 kcal/mol
Surface area73750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.295, 129.364, 192.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SidE


Mass: 96016.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6RCR1, UniProt: Q6BBR6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tacsimate

-
Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 63238 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.049 / Rrim(I) all: 0.173 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.75 Å / CC1/2: 0.885 / Rpim(I) all: 0.273 / Rrim(I) all: 0.98

-
Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQ5

5zq5


Resolution: 2.704→48.818 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25
RfactorNum. reflection% reflection
Rfree0.2475 3222 5.1 %
Rwork0.2025 --
obs0.2048 63238 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.704→48.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13091 0 0 150 13241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413347
X-RAY DIFFRACTIONf_angle_d0.77118030
X-RAY DIFFRACTIONf_dihedral_angle_d15.2455044
X-RAY DIFFRACTIONf_chiral_restr0.0521988
X-RAY DIFFRACTIONf_plane_restr0.0042365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7044-2.74480.30171180.25532181X-RAY DIFFRACTION84
2.7448-2.78760.33181380.2582564X-RAY DIFFRACTION99
2.7876-2.83330.34091320.26432604X-RAY DIFFRACTION99
2.8333-2.88220.321490.2522565X-RAY DIFFRACTION100
2.8822-2.93460.36631390.25332605X-RAY DIFFRACTION100
2.9346-2.9910.32411380.25212583X-RAY DIFFRACTION100
2.991-3.05210.31411430.25642623X-RAY DIFFRACTION100
3.0521-3.11840.33231340.24152581X-RAY DIFFRACTION100
3.1184-3.1910.30031440.24432603X-RAY DIFFRACTION100
3.191-3.27070.31591380.23832604X-RAY DIFFRACTION100
3.2707-3.35910.29171410.22042604X-RAY DIFFRACTION100
3.3591-3.4580.2611170.21142646X-RAY DIFFRACTION100
3.458-3.56960.29061450.20252638X-RAY DIFFRACTION100
3.5696-3.69710.22811250.19282634X-RAY DIFFRACTION100
3.6971-3.84510.22531430.18892586X-RAY DIFFRACTION100
3.8451-4.020.22531240.17332662X-RAY DIFFRACTION100
4.02-4.23180.18071360.1692629X-RAY DIFFRACTION100
4.2318-4.49680.18961510.15982620X-RAY DIFFRACTION100
4.4968-4.84370.19461910.16012620X-RAY DIFFRACTION100
4.8437-5.33060.18961490.17162643X-RAY DIFFRACTION100
5.3306-6.10070.20761360.19972707X-RAY DIFFRACTION100
6.1007-7.68140.26231500.20362699X-RAY DIFFRACTION100
7.6814-48.82570.22851410.19532815X-RAY DIFFRACTION99

+
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