8YV7 | pdb_00008yv7

X-ray structure of Thialysine N-epsilon-acetyltransferase from Caenorhabditis elegans

• PDB DOI: https://doi.org/10.2210/pdb8YV7/pdb

• Classification: TRANSFERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-28 Released: 2025-04-02 
• Deposition Author(s): Wang, N., Ma, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free: 
  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Biosynthesis of N-epsilon-acetyl-lysine by GNAT

Wang, N., Ma, X.

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: homology

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: 74.69 kDa 
• Atom Count: 5,261 
• Modeled Residue Count: 640 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thialysine N-epsilon-acetyltransferase	A, B, C, D	160	Caenorhabditis elegans	Mutation(s): 0  Gene Names: D2023.4 EC: 2.3.1
UniProt
Find proteins for O17731 (Caenorhabditis elegans) Explore O17731  Go to UniProtKB:  O17731

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.38 Å
• R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.329	α = 80.62
b = 65.098	β = 72.76
c = 65.322	γ = 63.98

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Wang, N., Ma, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22377058

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release