#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2013 Title: Crystallization and sulfur SAD phasing of AggA, the major subunit of aggregative adherence fimbriae type I from the Escherichia coli strain that caused an outbreak of haemolytic-uraemic syndrome in Germany. Authors: Pakharukova, N. / Tuittila, M. / Zavialov, A.
biological unit is a fimbriae made of polymerised of AggA subunits, and on the tip of the fimbriae minor subunit (AggB) is located. Assymmetric unit consists of two AggA subunits
-
Components
#1: Protein
AggregativeadherencefimbrialsubunitAggA / Aggregative adherence fimbriae / type I (AAF/I) / major subunit / AggA / Shiga-toxin producing E.coli
Mass: 16768.891 Da / Num. of mol.: 2 / Fragment: Residues 41-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O104:H4 str. C227-11 (bacteria) Gene: EUAG_05069 / Plasmid: pET101D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: G5TBZ9
Method to determine structure: SAD / Resolution: 1.55→55.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2224 / WRfactor Rwork: 0.1503 / FOM work R set: 0.8261 / SU B: 4.706 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1125 / SU Rfree: 0.1005 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2319
1854
4.9 %
RANDOM
Rwork
0.1562
36021
-
-
obs
0.1598
37875
90.68 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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