Journal: Biochemistry / Year: 2010 Title: Structural Basis for Inverting the Enantioselectivity of Arylmalonate Decarboxylase Revealed by the Structural Analysis of the Gly74Cys/Cys188Ser Mutant in the Liganded Form Authors: Obata, R. / Nakasako, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystallization and preliminary X-ray diffraction experiments of arylmalonate decarboxylase from Alcaligenes bronchisepticus Authors: Nakasako, M. / Obata, R. / Okubo, R. / Nakayama, S. / Miyamoto, K. / Ohta, H.
History
Deposition
Jul 16, 2008
Deposition site: RCSB / Processing site: PDBJ
Revision 1.0
Jul 21, 2009
Provider: repository / Type: Initial release
Revision 1.1
Jul 13, 2011
Group: Advisory / Derived calculations / Version format compliance
THOUGH FOUR MOLECULES OCCUPIED THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, SMALL-ANGLE X=RAY SCATTERING MEASUREMENT OF THE ENZYME SOLUTION REVEALED THAT THE FUNCTIONAL UNIT OF THE ENZYME IN SOLUTION WAS MONOMER. THIS POINT IS REPORTED IN REFERENCE 1 OF REMARK 1
-
Components
-
Arylmalonate ... , 3 types, 4 molecules ABCD
#1: Protein
Arylmalonatedecarboxylase / AMDase
Mass: 24755.357 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: KU1201 / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase
#2: Protein
Arylmalonatedecarboxylase / AMDase
Mass: 24831.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase
#3: Protein
Arylmalonatedecarboxylase / AMDase
Mass: 24831.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Plasmid: pAMD 101 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha-MCR / References: UniProt: Q05115, arylmalonate decarboxylase
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