› 5dar

X-ray diffraction
2.9Å resolution

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII

Released:
DOI: 10.2210/pdb5dar/pdb
PDB 5dar coloured by chain and viewed from the front.
PDB 5dar coloured by chain and viewed from the side.
PDB 5dar coloured by chain and viewed from the top.
Source organism: Methanocaldococcus jannaschii
Entry authors: Gabdulkhakov AG, Mitroshin IV, Garber MB

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
50S ribosomal protein L10 Chains: B, E
Molecule details ›
Chains: B, E
Length: 213 amino acids
Theoretical weight: 23.35 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P54049 (Residues: 9-221; Coverage: 63%)
Gene names: MJ0509, rpl10, rplP0
Sequence domains:
Structure domains:
50S ribosomal protein L11 Chains: C, F
Molecule details ›
Chains: C, F
Length: 161 amino acids
Theoretical weight: 17.51 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P54030 (Residues: 1-161; Coverage: 100%)
Gene names: MJ0373, rpl11
Sequence domains:
Structure domains: Ribosomal protein L11/L12, N-terminal domain
74 nt fragment of 23S rRNA Chains: A, D
Molecule details ›
Chains: A, D
Length: 74 nucleotides
Theoretical weight: 23.93 KDa
Sequence domains: Archaeal large subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 8 x MG
Ligand CL 3 x CL
Ligand K 5 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P21
Unit cell:
a: 72.396Å b: 88.451Å c: 95.231Å
α: 90° β: 102.19° γ: 90°
R-values:
R R work R free
0.266 0.264 0.297
Expression system: Escherichia coli BL21(DE3)

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