2OKL

Crystal structure of Peptide Deformylase 2 with actinonin from Bacillus cereus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

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This is version 1.2 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

  • DOI: https://doi.org/10.5483/bmbrep.2007.40.6.1050
  • Primary Citation of Related Structures:  
    2OKL

  • 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, 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase 2
A, B
185Bacillus cereus ATCC 14579Mutation(s): 0 
Gene Names: def2
EC: 3.5.1.88
UniProt
Find proteins for Q819K2 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711))
Explore Q819K2 
Go to UniProtKB:  Q819K2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ819K2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.447α = 90
b = 69.447β = 90
c = 294.412γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations