› 1dfu

X-ray diffraction
1.8Å resolution

CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION

Released:
DOI: 10.2210/pdb1dfu/pdb
PDB entry 1dfu coloured by chain, front view.
PDB entry 1dfu coloured by chain, side view.
PDB entry 1dfu coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
Lu M, Steitz TA
Proc. Natl. Acad. Sci. U.S.A. 97 2023-8 (2000)
PMID: 10696113

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159549 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Large ribosomal subunit protein bL25 Chain: P
Molecule details ›
Chain: P
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P68919 (Residues: 1-94; Coverage: 100%)
Gene names: JW2173, b2185, rplY
Sequence domains: Ribosomal L25p family
Structure domains: Ribosomal Protein L25; Chain P
5S ribosomal RNA Chain: M
Molecule details ›
Chain: M
Length: 19 nucleotides
Theoretical weight: 6.16 KDa
Source organism: Escherichia coli
Expression system: Not provided
5S ribosomal RNA Chain: N
Molecule details ›
Chain: N
Length: 19 nucleotides
Theoretical weight: 6.21 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 5 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: C2221
Unit cell:
a: 75.6Å b: 76.6Å c: 95.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.225
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

NMR spectroscopy of RNA.
Fürtig et al. (2003)
7 more

27 mentions without citation

The natural history of ubiquitin and ubiquitin-related domains.
Burroughs et al. (2012)
26 more