6C55

Crystal structure of Staphylococcus aureus Ketol-acid Reductosimerrase with hydroxyoxamate inhibitor 3

• PDB DOI: https://doi.org/10.2210/pdb6C55/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus RF122
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-01-14 Released: 2019-01-16 
• Deposition Author(s): Kandale, A., Patel, K.M., Zheng, S., You, L., Guddat, L.W., Schenk, G., Schmbri, M., McGeary, R.P.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.206 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

Design, synthesis, in vitro activity and crystallisation of novel N-isopropyl-N-hydroxyoxamate derivatives as ketol-acid reductoisomerase (KARI) inhibitors

Kandale, A., Patel, K.M., Zheng, S., You, L., Guddat, L.W., Schenk, G., Schmbri, M., McGeary, R.P.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 77.89 kDa 
• Atom Count: 5,590 
• Modelled Residue Count: 652 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+))	A, B	340	Staphylococcus aureus RF122	Mutation(s): 0  Gene Names: ilvC, SAB1941 EC: 1.1.1.86
UniProt
Find proteins for Q2YUF3 (Staphylococcus aureus (strain bovine RF122 / ET3-1)) Explore Q2YUF3  Go to UniProtKB:  Q2YUF3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
EKA	I [auth A]	[cyclohexyl(hydroxy)amino](oxo)acetic acid C8 H13 N O4 HMDGECZILRJLEV-UHFFFAOYSA-N
EKD	F [auth A], H [auth A]	(cyclohexylamino)(oxo)acetic acid C8 H13 N O3 JXKXKOUBASQQOF-UHFFFAOYSA-N
MG	C [auth A], D [auth A], G [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.206 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.724	α = 90
b = 79.032	β = 101.39
c = 69.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Kandale, A., Patel, K.M., Zheng, S., You, L., Guddat, L.W., Schenk, G., Schmbri, M., McGeary, R.P.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description