- PDB-1d6m: CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1d6m
Title
CRYSTAL STRUCTURE OF E. COLI DNA TOPOISOMERASE III
Components
DNA TOPOISOMERASE IIITopoisomerase
Keywords
ISOMERASE / DNA TOPOISOMERASE / DECATENATING ENZYME
Function / homology
Function and homology information
cytoplasmic replication fork / sequence-specific single stranded DNA binding / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA-templated DNA replication / DNA recombination / DNA repair / magnesium ion binding Similarity search - Function
DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 ...DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / Topoisomerase I; domain 3 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 3→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 24861467.8 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Refinement done with REFMAC. The solvent correction was calculated with XPLOR and applied in REFMAC. Final parameters obtained with CNS 0.4
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.268
1643
5 %
RANDOM
Rwork
0.237
-
-
-
all
0.239
32569
-
-
obs
0.239
32569
93.6 %
-
Displacement parameters
Biso mean: 51.9 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.92 Å2
8.16 Å2
0 Å2
2-
-
1.92 Å2
0 Å2
3-
-
-
-3.84 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.43 Å
0.37 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.61 Å
0.44 Å
Refinement step
Cycle: LAST / Resolution: 3→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4798
0
0
0
4798
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
p_angle_d
2.3
X-RAY DIFFRACTION
p_bond_d
0.007
LS refinement shell
Resolution: 3→3.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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