6JET | pdb_00006jet

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

• PDB DOI: https://doi.org/10.2210/pdb6JET/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii MRSN 3527
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-07 Released: 2020-02-12 
• Deposition Author(s): Ho, T.H., Lee, I.H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

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

Ho, T.H., Lee, I.H., Kang, L.W.

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: 39.91 kDa 
• Atom Count: 2,651 
• Modeled Residue Count: 341 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B	171	Acinetobacter baumannii MRSN 3527	Mutation(s): 0  Gene Names: def_1, def, T630_0214 EC: 3.5.1.88
UniProt
Find proteins for B0VNL8 (Acinetobacter baumannii (strain SDF)) Explore B0VNL8  Go to UniProtKB:  B0VNL8

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: 2.60 Å
• R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.666	α = 90
b = 112.903	β = 102.85
c = 43.678	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): 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