› 4tzv

X-ray diffraction
5.03Å resolution

Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization

Released:
DOI: 10.2210/pdb4tzv/pdb
PDB entry 4tzv coloured by chain, front view.
PDB entry 4tzv coloured by chain, side view.
PDB entry 4tzv coloured by chain, top view.
Source organisms:
Primary publication:
Dramatic improvement of crystals of large RNAs by cation replacement and dehydration.
Zhang J, Ferré-D'Amaré AR
Structure 22 1363-1371 (2014)
PMID: 25185828

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155456 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
RNA-binding protein YbxF Chain: A
Molecule details ›
Chain: A
Length: 82 amino acids
Theoretical weight: 8.49 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P46350 (Residues: 2-82; Coverage: 99%)
Gene names: BSU01090, rplGB, rulS, ybaB, ybxF
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
engineered tRNA Chain: B
Molecule details ›
Chain: B
Length: 75 nucleotides
Theoretical weight: 24.26 KDa
Source organism: Bacillus subtilis
Expression system: Not provided
Sequence domains: tRNA
T-box stem I Chain: C
Molecule details ›
Chain: C
Length: 102 nucleotides
Theoretical weight: 33.11 KDa
Source organism: Oceanobacillus iheyensis HTE831
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P43212
Unit cell:
a: 75.742Å b: 75.742Å c: 270.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.282 0.278 0.325
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

4 review citations

Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.
Sun et al. (2017)
3 more

4 mentions without citation

Dramatic improvement of crystals of large RNAs by cation replacement and dehydration.
Zhang et al. (2014)
3 more