[English] 日本語
Yorodumi
- PDB-7ew8: Legionella pneumophila effector AnkD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ew8
TitleLegionella pneumophila effector AnkD
ComponentsANK_REP_REGION domain-containing protein
KeywordsTOXIN / Legionella pneumophila effector / Lipid droplet / vesicle trafficking
Function / homologyAnkyrin repeat profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.594 Å
AuthorsChen, T.T. / Lin, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2022
Title: Atypical Legionella GTPase effector hijacks host vesicular transport factor p115 to regulate host lipid droplet.
Authors: Chen, T.T. / Lin, Y. / Zhang, S. / Liu, S. / Song, L. / Zhong, W. / Luo, Z.Q. / Han, A.
History
DepositionMay 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANK_REP_REGION domain-containing protein
B: ANK_REP_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)110,3272
Polymers110,3272
Non-polymers00
Water2,702150
1
A: ANK_REP_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)55,1641
Polymers55,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANK_REP_REGION domain-containing protein


Theoretical massNumber of molelcules
Total (without water)55,1641
Polymers55,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.058, 75.997, 104.814
Angle α, β, γ (deg.)90.000, 90.810, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ANK_REP_REGION domain-containing protein / AnkD


Mass: 55163.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12350, DI026_04400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F2G5
#2: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, Bis Tris, PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 32269 / % possible obs: 92.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 15131 / CC1/2: 0.843 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.594→45.207 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 1485 4.95 %
Rwork0.201 28529 -
obs0.2043 32269 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.1 Å2 / Biso mean: 49.8776 Å2 / Biso min: 11.44 Å2
Refinement stepCycle: final / Resolution: 2.594→45.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6676 0 0 150 6826
Biso mean---38.29 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096854
X-RAY DIFFRACTIONf_angle_d1.1169212
X-RAY DIFFRACTIONf_chiral_restr0.052996
X-RAY DIFFRACTIONf_plane_restr0.0081218
X-RAY DIFFRACTIONf_dihedral_angle_d3.6284256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5942-2.6780.3595660.2413178664
2.678-2.77370.28661170.2239210076
2.7737-2.88470.28131660.2385236186
2.8847-3.0160.29981270.238265795
3.016-3.17490.35121260.2499277799
3.1749-3.37380.27671400.21672781100
3.3738-3.63420.30261640.21492767100
3.6342-3.99970.27551330.18842816100
3.9997-4.5780.25251470.1732793100
4.578-5.76590.23231710.18412793100
5.7659-45.2070.22111280.17962898100

+
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://pdbjlvh1.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