› 5v4d

X-ray diffraction
1.6Å resolution

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfA from Yersinia pestis

Released:
DOI: 10.2210/pdb5v4d/pdb
PDB entry 5v4d coloured by chain, front view.
PDB entry 5v4d coloured by chain, side view.
PDB entry 5v4d coloured by chain, top view.
Source organism: Yersinia pestis
Entry authors: Kim Y, Chhor G, Endres M, Krishnan A, Babnigg G, Schneewind O, Anderson WF, Joachimiak A, Center for Structural Genomics of Infectious Diseases (CSGID)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-497464 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Translational inhibitor protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 128 amino acids
Theoretical weight: 13.71 KDa
Source organism: Yersinia pestis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A3N4B564 (Residues: 2-126; Coverage: 99%)
Gene name: YPO0627
Sequence domains: Endoribonuclease L-PSP
Structure domains: RutC-like

Ligands and Environments

3 bound ligands:
Ligand ACY 7 x ACY
Ligand CA 6 x CA
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 67.927Å b: 80.919Å c: 141.929Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.154 0.153 0.18
Expression system: Escherichia coli BL21(DE3)

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