› 1zde

X-ray diffraction
1.95Å resolution

1.95 Angstrom Crystal Structure of a dnaE Intein Precursor from Synechocystis Sp. Pcc 6803

Released:
DOI: 10.2210/pdb1zde/pdb
PDB entry 1zde coloured by chain, front view.
PDB entry 1zde coloured by chain, side view.
PDB entry 1zde coloured by chain, top view.
Source organism: Synechocystis sp. PCC 6803
Primary publication:
Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing.
Sun P, Ye S, Ferrandon S, Evans TC, Xu MQ, Rao Z
J Mol Biol 353 1093-105 (2005)
PMID: 16219320

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159948 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ssp dnaE intein, 1st part Chain: A
Molecule details ›
Chain: A
Length: 177 amino acids
Theoretical weight: 19.81 KDa
Source organism: Synechocystis sp. PCC 6803
Expression system: Escherichia coli
UniProt:
  • Canonical: P74750 (Residues: 770-936; Coverage: 12%)
Gene names: dnaE-C, dnaE-N, sll1572, slr0603
Structure domains: Hedgehog/Intein (Hint) domain

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BSRF BEAMLINE 3W1A
Spacegroup: P212121
Unit cell:
a: 42.489Å b: 58.224Å c: 67.124Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.195 0.222
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Protein splicing in cis and in trans.
Saleh et al. (2006)
8 more

7 mentions without citation

Chemoenzymatic Semisynthesis of Proteins.
Thompson et al. (2020)
6 more