6IL0

K3U complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae

• PDB DOI:  https://doi.org/10.2210/pdb6IL0/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-16 Released: 2019-10-23 
• Deposition Author(s): Lee, I.H., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.231 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

FBIs complex structure of peptide deformylase from Xanthomonas oryzae pv. oryzae

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)

Macromolecule Content

• Total Structure Weight: 19.44 kDa 
• Atom Count: 1,318 
• Modelled Residue Count: 160 
• Deposited Residue Count: 169 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	169	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 0  Gene Names: def, XOO1075 EC: 3.5.1.88

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K3U	B [auth A]	S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate C19 H17 F3 O2 S CADIQQIULRUWPM-MRXNPFEDSA-N
NI	C [auth A], D [auth A], E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.231 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.682	α = 90
b = 58.682	β = 90
c = 265.531	γ = 120

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: 2019-10-23 
Deposition Author(s): Lee, I.H., Kang, L.W.

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release