2IP6

Crystal structure of PedB

PDB DOI: https://doi.org/10.2210/pdb2IP6/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Pediococcus pentosaceus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2006-10-12 Released: 2007-10-02
Deposition Author(s): Kang, S.O., Kim, I.K., Kim, M.K., Kim, J.H., Yim, H.S., Cha, S.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.230
R-Value Work: 0.209
R-Value Observed: 0.209

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

High resolution crystal structure of PedB: a structural basis for the classification of pediocin-like immunity proteins

Kim, I.K., Kim, M.K., Kim, J.H., Yim, H.S., Cha, S.S., Kang, S.O.

(2007) BMC Struct Biol 7: 35-35

PubMed: 17537233 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1472-6807-7-35
Primary Citation of Related Structures:
2IP6

PubMed Abstract:
Pediocin-like bacteriocins, ribosomally-synthesized antimicrobial peptides, are generally coexpressed with cognate immunity proteins in order to protect the bacteriocin-producer from its own bacteriocin. As a step for understanding the mode of action of immunity proteins, we determined the crystal structure of PedB, a pediocin-like immunity protein conferring immunity to pediocin PP-1.

Organizational Affiliation

Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea. ikkim33@snu.ac.kr

Macromolecule Content

Total Structure Weight: 13.11 kDa
Atom Count: 867
Modelled Residue Count: 87
Deposited Residue Count: 112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PapB	A	112	Pediococcus pentosaceus	Mutation(s): 0
UniProt
Find proteins for Q79IK2 (Pediococcus pentosaceus) Explore Q79IK2 Go to UniProtKB: Q79IK2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q79IK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]