structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Representative
Model #1
combination of factors
-
Components
#1: Protein
5,10-methenyltetrahydrofolatesynthetase
Mass: 22361.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1731 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK References: UniProt: O67621, 5-formyltetrahydrofolate cyclo-ligase
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
3D 15N-separated NOESY
1
2
1
3D 13C-separated NOESY
1
3
3
4D 13C-separated NOESY
1
4
1
HNHA
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
1 mM 5,10-methenyltetrahydrofolate synthetase U-15N,13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3 pH 6.5 95% H2O, 5% D2O
95% H2O/5% D2O
2
0.5 mM 5,10-methenyltetrahydrofolate synthetase U-15N,5%-13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3 pH 6.5 95% H2O, 5% D2O
95% H2O/5% D2O
3
1 mM 5,10-methenyltetrahydrofolate synthetase U-15N,13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3 pH 6.5 100% D2O
Method: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1 Details: FINAL REFINEMENT IN EXPLICIT SOLVENT WITH LEONARD-JONES AND ELECTROSTATIC POTENTIALS. BACKBONE AND SIDECHAIN ASSIGNMENTS WERE DETERMINED MANUALLY FROM TRIPLE-RESONANCE NMR DATA. NOE DISTANCE ...Details: FINAL REFINEMENT IN EXPLICIT SOLVENT WITH LEONARD-JONES AND ELECTROSTATIC POTENTIALS. BACKBONE AND SIDECHAIN ASSIGNMENTS WERE DETERMINED MANUALLY FROM TRIPLE-RESONANCE NMR DATA. NOE DISTANCE RESTRAINTS WERE DERIVED MANUALLY FROM NOESY DATA. THE STRUCTURE IS BASED ON 1235 RESTRAINTS: 938 NOE DISTANCE RESTRAINTS, 112 H-BOND RESTRAINTS (56 H-BONDS), AND 185 DIHEDRAL RESTRAINTS. PHI DIHEDRAL RESTRAINTS WERE DERIVED FROM THE HNHA EXPERIMENT AND TALOS. PSI DIHEDRAL RESTRAINTS WERE DERIVED FROM NOE RATIOS, SECONDARY STRUCTURE PROPENSITIES EVIDENT IN PRELIMINARY STRUCTURES, ALPHA CARBON CHEMICAL SHIFTS, AND TALOS. RESIDUES 1-2 AND 182-194 ARE UNSTRUCTURED TERMINI IN THIS ENSEMBLE.
NMR representative
Selection criteria: combination of factors
NMR ensemble
Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 29 / Conformers submitted total number: 20
+
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