6JF6

Met-ala-ser bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6JF6/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-08 Released: 2020-02-12 
• Deposition Author(s): Jung, K.H., Ho, T.H., Lee, I.H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.292 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 

Literature

Met-ala-ser bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

Jung, K.H., Ho, T.H., Lee, I.H., Kang, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.63 kDa 
• Atom Count: 4,961 
• Modelled Residue Count: 634 
• Deposited Residue Count: 643 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	160	Acinetobacter baumannii	Mutation(s): 0  Gene Names: def, C3415_07350, IX87_00730 EC: 3.5.1.88

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MET-ALA-SER	E	3	synthetic construct	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.292 
• R-Value Work: 0.210 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.37	α = 90
b = 39.347	β = 89.98
c = 110.353	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Jung, K.H., Ho, T.H., Lee, I.H., Kang, L.W.

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description