6KVS | pdb_00006kvs

Staphylococcus aureus FabH with covalent inhibitor Oxa1

• PDB DOI: https://doi.org/10.2210/pdb6KVS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Staphylococcus aureus subsp. aureus Mu3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-05 Released: 2020-09-09 
• Deposition Author(s): Yuan, Y., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of S. aureus FabH, beta-ketoacyl carrier protein synthase

Qiu, X., Choudhry, A.E.

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: 68.37 kDa 
• Atom Count: 5,091 
• Modeled Residue Count: 626 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3	A, B	313	Staphylococcus aureus subsp. aureus Mu3	Mutation(s): 0  Gene Names: fabH, SAHV_0978 EC: 2.3.1.180
UniProt
Find proteins for A7X0K2 (Staphylococcus aureus (strain Mu3 / ATCC 700698)) Explore A7X0K2  Go to UniProtKB:  A7X0K2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAX	C [auth A], D [auth B]	4-chloranyl-N-[[cyclopropylmethyl(methanoyl)amino]methyl]benzamide C13 H15 Cl N2 O2 ZKBKHQJPIDEDKI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.754	α = 90
b = 91.573	β = 90
c = 109.811	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Yuan, Y., Wang, J.

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary