3FWX

The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor str. N16961

• PDB DOI: https://doi.org/10.2210/pdb3FWX/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-19 Released: 2009-03-17 
• Deposition Author(s): Zhang, R., Zhou, M., Stam, J., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.262 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Literature

The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor

Zhang, R., Zhou, M., Stam, J., Anderson, W., Joachimiak, A.

To be published.

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: 38.85 kDa 
• Atom Count: 2,911 
• Modelled Residue Count: 330 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	169	Vibrio cholerae O395	Mutation(s): 0  Gene Names: def-1, GI:15640078, VC0395_A2473 EC: 3.5.1.88
UniProt
Find proteins for Q9KVU3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVU3  Go to UniProtKB:  Q9KVU3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.262 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.305	α = 90
b = 61.456	β = 90
c = 210.343	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Zhang, R., Zhou, M., Stam, J., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary