9F5Q

Crystal structure of selenomethionine-labelled kinetoplastid kinetochore protein KKT23 acetyltransferase domain from Trypanosoma brucei

PDB DOI: https://doi.org/10.2210/pdb9F5Q/pdb

Classification: CELL CYCLE
Organism(s): Trypanosoma brucei brucei TREU927
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-30 Released: 2024-08-28
Deposition Author(s): Ludzia, P., Ishii, M., Akiyoshi, B.
Funding Organization(s): Wellcome Trust, Boehringer Ingelheim Fonds (BIF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.227
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail

Ludzia, P., Ishii, M., Akiyoshi, B.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.08.16.608276

Macromolecule Content

Total Structure Weight: 54.32 kDa
Atom Count: 3,681
Modelled Residue Count: 424
Deposited Residue Count: 448
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyltransferase domain-containing protein	A, B	224	Trypanosoma brucei brucei TREU927	Mutation(s): 0 Gene Names: Tb10.70.0180
UniProt
Find proteins for Q38AU6 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38AU6 Go to UniProtKB: Q38AU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q38AU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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: 0.227
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.299	α = 100.54
b = 44.528	β = 103.17
c = 68.969	γ = 101.33

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	210622/Z/18/Z/WT
Boehringer Ingelheim Fonds (BIF)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2024-08-28
Type: Initial release

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.