3DR6 | pdb_00003dr6

Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb3DR6/pdb

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


• Deposited: 2008-07-10 Released: 2008-09-09 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.200 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Funded by the national institute of allergy and infectious diseases of nih (contract number hhsn272200700058c).

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.49 kDa 
• Atom Count: 4,997 
• Modeled Residue Count: 511 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
yncA	A, B, C	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth B], H [auth B], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.200 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33dr6

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.898	α = 90
b = 70.229	β = 102.64
c = 59.157	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: 2008-09-09 
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: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, 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: 2024-11-20
  Changes: Structure summary