› 6nz6

X-ray diffraction
1.95Å resolution

YcjX-GDP (type II)

Released:
DOI: 10.2210/pdb6nz6/pdb
PDB entry 6nz6 coloured by chain, front view.
PDB entry 6nz6 coloured by chain, side view.
PDB entry 6nz6 coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.
Tsai JT, Sung N, Lee J, Chang C, Lee S, Tsai FTF
J Mol Biol 431 3179-3190 (2019)
PMID: 31202886

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-568432 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ras-like GTPase YcjX Chains: A, B
Molecule details ›
Chains: A, B
Length: 485 amino acids
Theoretical weight: 54.46 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8EG04 (Residues: 1-485; Coverage: 100%)
Gene names: SO_1810, ycjX
Sequence domains: YcjX-like family, DUF463

Ligands and Environments

1 bound ligand:
Ligand GDP 2 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 59.385Å b: 134.1Å c: 145.024Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.162 0.205
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes.
Niu et al. (2020)

1 mention without citation

Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.
Tsai et al. (2019)