2OS3 | pdb_00002os3

Structures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes

• PDB DOI: https://doi.org/10.2210/pdb2OS3/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes M1 GAS
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-05 Released: 2008-03-04 
• Deposition Author(s): Kim, E.E., Kim, K.-H., Moon, J.H., Choi, K., Lee, H.K., Parh, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.205 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structures of actinonin bound peptide deformylases from E. faecalis and S. pyogenes

Kim, E.E., Kim, K.-H., Moon, J.H., Choi, K., Lee, H.K., Park, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.45 kDa 
• Atom Count: 1,791 
• Modeled Residue Count: 205 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	205	Streptococcus pyogenes M1 GAS	Mutation(s): 0  Gene Names: def EC: 3.5.1.88
UniProt
Find proteins for P68771 (Streptococcus pyogenes serotype M1) Explore P68771  Go to UniProtKB:  P68771

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	C [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.205 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.557	α = 90
b = 40.557	β = 90
c = 217.938	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Kim, E.E., Kim, K.-H., Moon, J.H., Choi, K., Lee, H.K., Parh, H.S.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description