› 3his

X-ray diffraction
1.49Å resolution

Crystal structure of Saporin-L1 from Saponaria officinalis

Released:
DOI: 10.2210/pdb3his/pdb
PDB entry 3his coloured by chain, front view.
PDB entry 3his coloured by chain, side view.
PDB entry 3his coloured by chain, top view.
Source organism: Saponaria officinalis
Primary publication:
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Ho MC, Sturm MB, Almo SC, Schramm VL
Proc Natl Acad Sci U S A 106 20276-81 (2009)
PMID: 19920175

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-173880 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
rRNA N-glycosylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 259 amino acids
Theoretical weight: 28.77 KDa
Source organism: Saponaria officinalis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q2QEH4 (Residues: 22-280; Coverage: 93%)
Sequence domains: Ribosome inactivating protein
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P1
Unit cell:
a: 50.939Å b: 53.058Å c: 54.632Å
α: 78.86° β: 65.62° γ: 80.65°
R-values:
R R work R free
0.21 0.208 0.24
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes.
Schramm VL. (2011)
13 more

34 mentions without citation

Copper active sites in biology.
Solomon et al. (2014)
33 more