› 2ip6

X-ray diffraction
1.35Å resolution

Crystal structure of PedB

Released:
DOI: 10.2210/pdb2ip6/pdb
PDB entry 2ip6 coloured by chain, front view.
PDB entry 2ip6 coloured by chain, side view.
PDB entry 2ip6 coloured by chain, top view.
Source organism: Pediococcus pentosaceus
Primary publication:
High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins.
Kim IK, Kim MK, Kim JH, Yim HS, Cha SS, Kang SO
BMC Struct Biol 7 35 (2007)
PMID: 17537233

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181267 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PapB Chain: A
Molecule details ›
Chain: A
Length: 112 amino acids
Theoretical weight: 13.01 KDa
Source organism: Pediococcus pentosaceus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q79IK2 (Residues: 1-112; Coverage: 100%)
Gene names: GBO79_09820, ITQ94_10035, papB, pedB
Sequence domains: Enterocin A Immunity
Structure domains: de novo design (two linked rop proteins)

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 6B
Spacegroup: P62
Unit cell:
a: 62.189Å b: 62.189Å c: 39.898Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.209 0.23
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

Class IIa bacteriocins: diversity and new developments.
Cui et al. (2012)
5 other articles

11 mentions without citation

Macromolecular ab initio phasing enforcing secondary and tertiary structure.
Millán et al. (2015)
10 more