› 2z53

X-ray diffraction
1.29Å resolution

Crystal structure of the S211A mutant of the ribosome inactivating protein PDL4 from P. dioica leaves

Released:
DOI: 10.2210/pdb2z53/pdb
PDB entry 2z53 coloured by chain, front view.
PDB entry 2z53 coloured by chain, side view.
PDB entry 2z53 coloured by chain, top view.
Source organism: Phytolacca dioica
Primary publication:
Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves.
Ruggiero A, Chambery A, Di Maro A, Parente A, Berisio R
Proteins 71 8-15 (2008)
PMID: 17963235

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160919 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosome-inactivating protein PD-L3/PD-L4 Chain: A
Molecule details ›
Chain: A
Length: 261 amino acids
Theoretical weight: 29.21 KDa
Source organism: Phytolacca dioica
Expression system: Escherichia coli
UniProt:
  • Canonical: P84854 (Residues: 1-261; Coverage: 100%)
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7A
Spacegroup: P212121
Unit cell:
a: 43.619Å b: 61.541Å c: 91.626Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.138 0.138 0.16
Expression system: Escherichia coli

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Citations

2 review citations

Ribosome-inactivating and related proteins.
Schrot et al. (2015)
1 more