Journal: Proteins / Year: 1998 Title: Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+. Authors: Berry, M.B. / Phillips Jr., G.N.
History
Deposition
Jun 7, 1996
Processing site: BNL
Revision 1.0
Jun 16, 1997
Provider: repository / Type: Initial release
Revision 1.1
Mar 24, 2008
Group: Version format compliance
Revision 1.2
Jul 13, 2011
Group: Version format compliance
Revision 1.3
Mar 7, 2018
Group: Data collection / Other / Category: diffrn_source / pdbx_database_status Item: _diffrn_source.source / _pdbx_database_status.process_site
Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details
ZINC FORMS A ZINC FINGER WITH CYS 130, CYS 133, CYS 150, AND CYS 153. IT APPEARS THAT THERE ARE TWO ...ZINC FORMS A ZINC FINGER WITH CYS 130, CYS 133, CYS 150, AND CYS 153. IT APPEARS THAT THERE ARE TWO ALTERNATE CONFORMATIONS FOR FOR THE GAMMA, DELTA, AND EPSILON PHOSPHATES OF HET GROUP AP5. THERE IS DENSITY FOR THE SECOND CONFORMATION OF THE DELTA PHOSPHATE BUT NOT FOR THE OTHERS. THUS ONLY ONE CONFORMATION IS PRESENTED FOR THE GAMMA AND EPSILON PHOSPHATES.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 1.97 Å3/Da / Density % sol: 43.5 %
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