[English] 日本語
Yorodumi
- PDB-2ixq: The solution structure of the invasive tip complex from Afa-Dr fibrils -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ixq
TitleThe solution structure of the invasive tip complex from Afa-Dr fibrils
Components
  • Afimbrial adhesin AFA-III
  • Protein AfaD
KeywordsCELL ADHESION / IG-LIKE DOMAIN / AFIMBRIAL SHEATH / STRUCTURAL PROTEIN / DONOR STRAND COMPLEMENTED / DAF / AFAE / UPEC / DAEC / FIMBRIA
Function / homology
Function and homology information


Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Adhesin, Dr-family / Adhesin, Dr family, signal peptide / Dr-family adhesin / Dr family adhesin / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like ...Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Adhesin, Dr-family / Adhesin, Dr family, signal peptide / Dr-family adhesin / Dr family adhesin / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein AfaD / Afimbrial adhesin AFA-III / AfaD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
Model type detailsMINIMIZED AVERAGE
AuthorsCota, E. / Jones, C. / Simpson, P. / Altroff, H. / Anderson, K.L. / du Merle, L. / Guignot, J. / Servin, A. / Le Bouguenec, C. / Mardon, H. / Matthews, S.
CitationJournal: Mol. Microbiol. / Year: 2006
Title: The solution structure of the invasive tip complex from Afa/Dr fibrils.
Authors: Cota, E. / Jones, C. / Simpson, P. / Altroff, H. / Anderson, K.L. / du Merle, L. / Guignot, J. / Servin, A. / Le Bouguenec, C. / Mardon, H. / Matthews, S.
History
DepositionJul 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 5, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_nmr_spectrometer / pdbx_validate_close_contact / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Oct 9, 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 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein AfaD
B: Afimbrial adhesin AFA-III


Theoretical massNumber of molelcules
Total (without water)30,7682
Polymers30,7682
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein Protein AfaD


Mass: 15311.866 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: afaD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47038, UniProt: Q7BG36*PLUS
#2: Protein Afimbrial adhesin AFA-III


Mass: 15456.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 38-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: afaE3, afaE-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57254
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

-
Sample preparation

Sample conditionsTemperature: 303.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

-
Processing

NMR softwareName: CNS
Developer: BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARREN
Classification: refinement
NMR ensembleConformers submitted total number: 1

+
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