› 3grv

X-ray diffraction
1.9Å resolution

Crystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1

Released:
DOI: 10.2210/pdb3grv/pdb
PDB entry 3grv coloured by chain, front view.
PDB entry 3grv coloured by chain, side view.
PDB entry 3grv coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design.
O'Farrell HC, Musayev FN, Scarsdale JN, Rife JP
Biochemistry 49 2697-704 (2010)
PMID: 20163168

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176617 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable ribosomal RNA small subunit methyltransferase A Chain: A
Molecule details ›
Chain: A
Length: 295 amino acids
Theoretical weight: 33.88 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58435 (Residues: 1-275; Coverage: 100%)
Gene names: MJ1029, ksgA, rsmA
Sequence domains: Ribosomal RNA adenine dimethylase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ADN 1 x ADN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P21
Unit cell:
a: 40.263Å b: 66.018Å c: 61.691Å
α: 90° β: 108.35° γ: 90°
R-values:
R R work R free
0.183 0.18 0.239
Expression system: Escherichia coli

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Citations

1 review citation

m6A-SAC-seq for quantitative whole transcriptome m6A profiling.
Ge et al. (2023)
5 other articles