› 4d79

X-ray diffraction
1.77Å resolution

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with ATP at 1.768 Angstroem resolution

Released:
DOI: 10.2210/pdb4d79/pdb
PDB entry 4d79 coloured by chain, front view.
PDB entry 4d79 coloured by chain, side view.
PDB entry 4d79 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily.
López-Estepa M, Ardá A, Savko M, Round A, Shepard WE, Bruix M, Coll M, Fernández FJ, Jiménez-Barbero J, Vega MC
PLoS One 10 e0118606 (2015)
PMID: 25897750

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175163 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA threonylcarbamoyladenosine dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 276 amino acids
Theoretical weight: 29.67 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q46927 (Residues: 1-268; Coverage: 100%)
Gene names: JW2783, b2812, csdL, tcdA, ygdL
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

4 bound ligands:
Ligand K 4 x K
Ligand ATP 4 x ATP
Ligand GOL 7 x GOL
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P21
Unit cell:
a: 65.69Å b: 97.16Å c: 83.19Å
α: 90° β: 111.61° γ: 90°
R-values:
R R work R free
0.144 0.142 0.183
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions.
Zheng et al. (2017)
4 other articles

3 mentions without citation

The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily.
López-Estepa et al. (2015)
2 more