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› 8x45

X-ray diffraction
2.5Å resolution

Crystal structure of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii (FormII)

Released:
DOI: 10.2210/pdb8x45/pdb
Model geometry
Fit model/data
PDB entry 8x45 coloured by chain, front view.
PDB entry 8x45 coloured by chain, side view.
PDB entry 8x45 coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Structural and functional characterization of archaeal DIMT1 unveils distinct protein dynamics essential for efficient catalysis.
Saha S, Kanaujia SP
Structure (2024)
PMID: 39146930

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-279360 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable ribosomal RNA small subunit methyltransferase A Chains: A, B
Molecule details ›
Chains: A, B
Length: 290 amino acids
Theoretical weight: 33.37 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O59487 (Residues: 1-268; Coverage: 100%)
Gene names: PH1823, ksgA, rsmA
Sequence domains: Ribosomal RNA adenine dimethylase

Ligands and Environments

8 bound ligands:
Ligand MTA 2 x MTA
Ligand ZN 5 x ZN
Ligand SO3 2 x SO3
Ligand GOL 2 x GOL
Ligand EDO 4 x EDO
Ligand PEG 2 x PEG
Ligand PGE 1 x PGE
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: C2
Unit cell:
a: 120.74Å b: 80.23Å c: 85.71Å
α: 90° β: 116.17° γ: 90°
R-values:
R R work R free
0.234 0.231 0.282
Expression system: Escherichia coli BL21(DE3)

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