2OKL

Crystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization of Peptide Deformylase2 from B. cereus

Park, J.K.Kim, K.H.Moon, J.H.Kim, E.E.

(2007) J.Biochem.Mol.Biol. 40: 1050-1057


  • PubMed Abstract: 
  • Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, ...

    Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.


    Organizational Affiliation

    Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-dong, Sungbuk-gu, Seoul 136-791, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase 2
A, B
185Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)Mutation(s): 0 
Gene Names: def2
EC: 3.5.1.88
Find proteins for Q819K2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711))
Go to UniProtKB:  Q819K2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
BB2
Query on BB2

Download SDF File 
Download CCD File 
A, B
ACTINONIN
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.447α = 90.00
b = 69.447β = 90.00
c = 294.412γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
CNSphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-01-17 
  • Released Date: 2008-01-15 
  • Deposition Author(s): Kim, E.E.

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance