› 6y4b

X-ray diffraction
5Å resolution

Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe

Released:
DOI: 10.2210/pdb6y4b/pdb
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PDB entry 6y4b coloured by chain, front view.
PDB entry 6y4b coloured by chain, side view.
PDB entry 6y4b coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.
Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E
OpenAccess logo RNA 26 1589-1602 (2020)
PMID: 32680846

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124261 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Cyclodipeptide synthase Chain: A
Molecule details ›
Chain: A
Length: 297 amino acids
Theoretical weight: 34.12 KDa
Source organism: Candidatus Glomeribacter gigasporarum BEG34
Expression system: Escherichia coli
UniProt:
  • Canonical: G2JBB2 (Residues: 1-291; Coverage: 100%)
Gene name: CAGGBEG34_30028
RNA (77-MER) Chain: F
Molecule details ›
Chain: F
Length: 76 nucleotides
Theoretical weight: 24.52 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand PHE 1 x PHE
4 modified residues:
Ligand 4SU 1 x 4SU
Ligand H2U 2 x H2U
Ligand PSU 3 x PSU
Ligand 5MU 1 x 5MU

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P6122
Unit cell:
a: 254.834Å b: 254.834Å c: 69.41Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.305 0.304 0.316
Expression system: Escherichia coli

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Citations

1 review citation

The diverse structural modes of tRNA binding and recognition.
Biela et al. (2023)
4 other articles

1 mention without citation

Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.
Bourgeois et al. (2020)

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