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- PDB-9f5q: Crystal structure of selenomethionine-labelled kinetoplastid kine... -

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Basic information

Entry
Database: PDB / ID: 9f5q
TitleCrystal structure of selenomethionine-labelled kinetoplastid kinetochore protein KKT23 acetyltransferase domain from Trypanosoma brucei
ComponentsN-acetyltransferase domain-containing protein
KeywordsCELL CYCLE / kinetochore / kinetoplastid / histone / acetyltransferase / mitosis
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / kinetochore / nucleus / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 4, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3234
Polymers52,7042
Non-polymers1,6192
Water3,153175
1
A: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1622
Polymers26,3521
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1622
Polymers26,3521
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.299, 44.528, 68.969
Angle α, β, γ (deg.)100.54, 103.17, 101.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein N-acetyltransferase domain-containing protein


Mass: 26352.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb10.70.0180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38AU6
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% v/v jeffamine M-2070, 20% v/v DMSO

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→29.53 Å / Num. obs: 32753 / % possible obs: 96.5 % / Redundancy: 3.6 % / CC1/2: 1 / Rrim(I) all: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2037 / CC1/2: 0.8 / Rrim(I) all: 0.704

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→29.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.701 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1614 4.9 %RANDOM
Rwork0.19849 ---
obs0.19982 31137 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.002 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å2-0.89 Å2-0.13 Å2
2--2.68 Å2-0.54 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.95→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 51 175 3681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123619
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163320
X-RAY DIFFRACTIONr_angle_refined_deg1.731.8334918
X-RAY DIFFRACTIONr_angle_other_deg0.5841.737633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.125525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44110532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9752.7331705
X-RAY DIFFRACTIONr_mcbond_other2.962.7331704
X-RAY DIFFRACTIONr_mcangle_it4.0694.8742120
X-RAY DIFFRACTIONr_mcangle_other4.0684.8772121
X-RAY DIFFRACTIONr_scbond_it4.5453.0511914
X-RAY DIFFRACTIONr_scbond_other4.4983.0551903
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2215.4432799
X-RAY DIFFRACTIONr_long_range_B_refined7.74930.844052
X-RAY DIFFRACTIONr_long_range_B_other7.73430.874032
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.953→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 109 -
Rwork0.278 1958 -
obs--83.21 %

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