› 2pxd

X-ray diffraction
2Å resolution

Variant 1 of Ribonucleoprotein Core of the E. Coli Signal Recognition Particle

Released:
DOI: 10.2210/pdb2pxd/pdb
PDB entry 2pxd coloured by chain, front view.
PDB entry 2pxd coloured by chain, side view.
PDB entry 2pxd coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A general strategy to solve the phase problem in RNA crystallography.
Keel AY, Rambo RP, Batey RT, Kieft JS
Structure 15 761-72 (2007)
PMID: 17637337

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-533309 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Signal recognition particle protein Chain: A
Molecule details ›
Chain: A
Length: 102 amino acids
Theoretical weight: 12.34 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AGD7 (Residues: 329-430; Coverage: 23%)
Gene names: JW5414, b2610, ffh
Sequence domains: Signal peptide binding domain
Structure domains: Signal recognition particle, SRP54 subunit, M-domain
4.5 S RNA Chain: B
Molecule details ›
Chain: B
Length: 49 nucleotides
Theoretical weight: 15.89 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NCO 7 x NCO
1 modified residue:
Ligand MSE 13 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 131.881Å b: 77.867Å c: 32.428Å
α: 90° β: 94.04° γ: 90°
R-values:
R R work R free
0.251 0.251 0.283
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

New molecular engineering approaches for crystallographic studies of large RNAs.
Zhang et al. (2014)
12 more

1 mention without citation

Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study.
Esmaeeli et al. (2021)