› 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 entry 5dar coloured by chain, front view.
PDB entry 5dar coloured by chain, side view.
PDB entry 5dar coloured by chain, top view.
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)
Assembly name:
PDBe Complex ID:
PDB-CPX-156928 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Large ribosomal subunit protein uL10 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:
Large ribosomal subunit protein uL11 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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