6JF3 | pdb_00006jf3

Actinonin bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6JF3/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Actinonin bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

Lee, I.H., Ho, T.H., Kang, L.W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.17 kDa 
• Atom Count: 2,321 
• Modeled Residue Count: 295 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	159	Acinetobacter baumannii	Mutation(s): 0  Gene Names: def, C3415_07350, IX87_00730 EC: 3.5.1.88

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2 (Subject of Investigation/LOI)	D [auth A], F [auth B]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.728	α = 90
b = 70.786	β = 90
c = 110.859	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): Lee, I.H., Ho, T.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