- PDB-1l2m: Minimized Average Structure of the N-terminal, DNA-binding domain... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1l2m
Title
Minimized Average Structure of the N-terminal, DNA-binding domain of the replication initiation protein from a geminivirus (Tomato yellow leaf curl virus-Sardinia)
Components
Rep protein
Keywords
VIRAL PROTEIN / a+b fold / RBD-like fold
Function / homology
Function and homology information
endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / host cell nucleus / structural molecule activity / DNA binding / ATP binding / metal ion binding Similarity search - Function
Geminivirus AL1, replication-associated protein / Geminivirus AL1 replication-associated protein, CLV type / Geminivirus AL1 replication-associated protein, central domain / Geminivirus Rep catalytic domain / Geminivirus rep protein central domain / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 13583.302 Da / Num. of mol.: 1 Fragment: N-terminal domain (residues 4-121), DNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato yellow leaf curl Sardinia virus / Genus: Begomovirus / Gene: rep / Production host: Escherichia coli (E. coli) / References: UniProt: P27260
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D NOESY
1
2
3
2D NOESY
1
3
1
3D 15N-separated NOESY
1
4
1
HNHA
1
5
1
HNHB
1
6
2
4D 13C/15N-separated NOESY
1
7
1
2D HN(CO)CG arom
1
8
1
2D HNCO arom
1
9
1
4D 13C,13C NOESY
NMR details
Text: This entry contains the minimized average structure of the 30-conformer ensemble deposited under code 1L5I. The single model included in this entry is a good representation of the 30-conformer ensemble.
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