3CMD

Crystal structure of peptide deformylase from VRE-E.faecium

• PDB DOI: https://doi.org/10.2210/pdb3CMD/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-21 Released: 2009-01-13 
• Deposition Author(s): Hwang, K.Y., Nam, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.229 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure.

Nam, K.H., Ham, J.I., Priyadarshi, A., Kim, E.E., Chung, N., Hwang, K.Y.

(2009) Proteins 74: 261-265

• PubMed: 18831047 
• DOI: https://doi.org/10.1002/prot.22257
• Primary Citation of Related Structures:  
  3CMD

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Organizational Affiliation: 

Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.25 kDa 
• Atom Count: 3,175 
• Modelled Residue Count: 374 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	196	Enterococcus faecium	Mutation(s): 0  EC: 3.5.1.88
UniProt
Find proteins for Q842S4 (Enterococcus faecium) Explore Q842S4  Go to UniProtKB:  Q842S4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	F [auth A], G [auth A], H [auth A], P [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
FE	C [auth A], I [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.229 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.47	α = 90
b = 149.47	β = 90
c = 143.329	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-13 
Deposition Author(s): Hwang, K.Y., Nam, K.H.

Revision History  

• Version 1.0: 2009-01-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description