endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta Similarity search - Domain/homology
Type: Bruker Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz
-
Processing
NMR software
Name
Version
Developer
Classification
CARA
1.8.4
KellerandWuthrich
dataanalysis
CNS
1.1
Brunger, Adams, Clore, Gros, NilgesandRead
refinement
CcpNmr Analysis
2.1
CCPN
structuresolution
CcpNmr Analysis
2.1
CCPN
dataanalysis
CcpNmr_Entry_Completion_Interface
2.1
PDBe & CCPN
dataanalysis
TopSpin
2.1
BrukerBiospin
structuresolution
UNIO
2
Herrmann, GuntertandWuthrich
structuresolution
CYANA
2.1
Guntert, MumenthalerandWuthrich
structuresolution
CYANA
2.1
Guntert, MumenthalerandWuthrich
refinement
Refinement
Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 Details: Initial structures were calculated using the ATNOS-CANDID module of UNIO employing CYANA. The UNIO derived constants were introduced to CNS using the RECOORD scripts for explicit water refinement.
NMR constraints
Hydrogen bond constraints total count: 114
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 80 / Conformers submitted total number: 10
+
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.
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