› 5d8h

X-ray diffraction
2.8Å resolution

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

Released:
DOI: 10.2210/pdb5d8h/pdb
PDB entry 5d8h coloured by chain, front view.
PDB entry 5d8h coloured by chain, side view.
PDB entry 5d8h coloured by chain, top view.
Source organisms:
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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-143181 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Large ribosomal subunit protein uL10 Chain: B
Molecule details ›
Chain: B
Length: 213 amino acids
Theoretical weight: 23.64 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 Chain: C
Molecule details ›
Chain: C
Length: 161 amino acids
Theoretical weight: 17.79 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
Thiostrepton Chain: D
Molecule details ›
Chain: D
Length: 19 amino acids
Theoretical weight: 1.81 KDa
Source organism: Streptomyces azureus
UniProt:
  • Canonical: P0C8P8 (Residues: 56-72; Coverage: 24%)
Gene name: tpdA
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 74 nucleotides
Theoretical weight: 23.93 KDa
Sequence domains: Archaeal large subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 11 x MG
Ligand NA 4 x NA
Ligand TRS 3 x TRS
7 modified residues:
Ligand MSE 12 x MSE
Ligand DHA 3 x DHA
Ligand BB9 4 x BB9
Ligand DBU 1 x DBU
Ligand DCY 1 x DCY
Ligand TS9 1 x TS9
Ligand MH6 1 x MH6

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: I222
Unit cell:
a: 125.07Å b: 127.16Å c: 132.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.245
Expression system: Escherichia coli BL21(DE3)

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