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)

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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8YV7

This is version 1.0 of the entry. See complete history.

Literature

Biosynthesis of N-epsilon-acetyl-lysine by GNAT

Wang, N., Ma, X.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O17731
Sequence Annotations Expand
Reference Sequence

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.