3DR8 | pdb_00003dr8

Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb3DR8/pdb

• Classification: TRANSFERASE
• Organism(s): Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-10 Released: 2008-08-12 
• Deposition Author(s): Singer, A.U., Skarina, T., Onopriyenko, O., Edwards, A.M., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.216 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA

Singer, A.U., Skarina, T., Onopriyenko, O., Edwards, A.M., Anderson, W.F., Savchenko, A.

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: 41.4 kDa 
• Atom Count: 3,299 
• Modeled Residue Count: 346 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
yncA	A, B	174	N/A	Mutation(s): 0  Gene Names: yncA EC: 2.3.1
UniProt
Find proteins for Q8ZPD3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPD3  Go to UniProtKB:  Q8ZPD3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	H [auth A], M [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
ACT	C [auth A], D [auth A], E [auth A], I [auth B], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A], G [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.216 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33dr8

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.254	α = 90
b = 71.374	β = 90
c = 74.005	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Singer, A.U., Skarina, T., Onopriyenko, O., Edwards, A.M., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary