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- PDB-9evr: Crystal structure of the kinetoplastid kinetochore protein KKT23 ... -

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Basic information

Entry
Database: PDB / ID: 9evr
TitleCrystal structure of the kinetoplastid kinetochore protein KKT23 N-terminal domain from Trypanosoma brucei
ComponentsN-acetyltransferase domain-containing protein
KeywordsCELL CYCLE / kinetochore / kinetoplastid / histone / acetyltransferase / mitosis
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / kinetochore / nucleus / cytoplasm / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.7 Å
AuthorsLudzia, P. / Ishii, M. / Akiyoshi, B.
Funding support United Kingdom, Germany, 2items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z/WT United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
Citation
Journal: Structure / Year: 2025
Title: The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail.
Authors: Ludzia, P. / Ishii, M. / Deak, G. / Spanos, C. / Wilson, M.D. / Redfield, C. / Akiyoshi, B.
#1: Journal: Biorxiv / Year: 2024
Title: The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail
Authors: Ludzia, P. / Ishii, M. / Akiyoshi, B.
History
DepositionApr 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Revision 1.2Jan 15, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)8,1041
Polymers8,1041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.338, 57.338, 83.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein N-acetyltransferase domain-containing protein


Mass: 8104.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 6HIS-KKT23 2-70
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb10.70.0180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38AU6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 1M Sodium phosphate, pH 6.5, 12% w/v PEG 8000

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→42.73 Å / Num. obs: 3165 / % possible obs: 100 % / Redundancy: 18.4 % / CC1/2: 1 / Rrim(I) all: 0.106 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.49-2.530.41480.79.3781
6.75-42.7355.719910.0291100

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Processing

Software
NameVersionClassification
PHENIX(1.20_4444: ???)refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.7→42.73 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.15 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 121 4.81 %
Rwork0.2453 --
obs0.2463 2517 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms386 0 0 0 386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.064
X-RAY DIFFRACTIONf_dihedral_angle_d4.60452
X-RAY DIFFRACTIONf_chiral_restr0.04757
X-RAY DIFFRACTIONf_plane_restr0.00769
LS refinement shellResolution: 2.7→42.73 Å
RfactorNum. reflection% reflection
Rfree0.2649 121 -
Rwork0.2453 2396 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -1.1699 Å / Origin y: -30.0489 Å / Origin z: 21.1297 Å
111213212223313233
T0.5156 Å20.0889 Å2-0.0693 Å2-0.4879 Å2-0.0274 Å2--0.4312 Å2
L0.0899 °2-0.0187 °2-0.0719 °2-0.0236 °20.0169 °2--0.0993 °2
S0.339 Å °0.0235 Å °0.3779 Å °-0.0329 Å °0.2177 Å °0.0205 Å °-0.3679 Å °0.18 Å °0.0021 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 17 through 64)

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