6JF5 | pdb_00006jf5

K2U bound crystal structure of class I type b peptide deformylase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb6JF5/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: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

K2U 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: 35.9 kDa 
• Atom Count: 2,405 
• Modeled Residue Count: 303 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A [auth B], B [auth A]	159	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  def_1, def, def2, def_2, ABUW_2937, APD06_18825, BWP00_08140, C2U32_01090, CBI29_01007, DCD77_14985, DGS69_13130, DOL94_15075, SAMEA104305268_00677, SAMEA104305292_01437, SAMEA104305351_01290 EC: 3.5.1.88
UniProt
Find proteins for A0A098SKQ8 (Acinetobacter baumannii) Explore A0A098SKQ8  Go to UniProtKB:  A0A098SKQ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K2U	D [auth B], F [auth A]	(3~{R},4~{R})-4-oxidanyl-3-(phenylmethyl)-4-(phenylmethylsulfanyl)butanoic acid C18 H20 O3 S OBXQOECJZPGJTO-SJLPKXTDSA-N
ZN	C [auth B], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.072	α = 90
b = 76.755	β = 90
c = 96.503	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
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