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

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Basic information

Entry
Database: PDB / ID: 9evq
TitleCrystal structure of the 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / Item: _pdbx_entry_details.has_protein_modification
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,8614
Polymers52,2422
Non-polymers1,6192
Water7,584421
1
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9312
Polymers26,1211
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9312
Polymers26,1211
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.266, 44.317, 68.815
Angle α, β, γ (deg.)100.508, 103.005, 101.322
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein N-acetyltransferase domain-containing protein


Mass: 26121.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 6HIS-KKT23 125-348
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.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium tartrate dibasic dehydrate, 0.1 M HEPES pH 7.0, 20% SOKOLAN PA 25 CL

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.63→65.16 Å / Num. obs: 55472 / % possible obs: 96 % / Redundancy: 3.6 % / Biso Wilson estimate: 18.67 Å2 / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 11.5
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3670 / CC1/2: 0.8 / Rrim(I) all: 0.741 / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→65.14 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.4781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 2004 4.99 %
Rwork0.1772 38192 -
obs0.1786 40196 85.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.15 Å2
Refinement stepCycle: LAST / Resolution: 1.75→65.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3465 0 102 421 3988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733679
X-RAY DIFFRACTIONf_angle_d1.09844997
X-RAY DIFFRACTIONf_chiral_restr0.059537
X-RAY DIFFRACTIONf_plane_restr0.0055616
X-RAY DIFFRACTIONf_dihedral_angle_d17.27211371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.2996780.26351459X-RAY DIFFRACTION45.83
1.79-1.840.2834990.24981781X-RAY DIFFRACTION56
1.84-1.90.30831060.23292249X-RAY DIFFRACTION70.96
1.9-1.960.22091500.20692798X-RAY DIFFRACTION88.13
1.96-2.030.23011570.19682878X-RAY DIFFRACTION89.85
2.03-2.110.24911520.18712961X-RAY DIFFRACTION93.54
2.11-2.20.22721670.17973008X-RAY DIFFRACTION95.12
2.2-2.320.22221530.17663009X-RAY DIFFRACTION95.15
2.32-2.470.22831570.17913024X-RAY DIFFRACTION95.44
2.47-2.660.20851570.19213040X-RAY DIFFRACTION95.92
2.66-2.920.22691650.1913018X-RAY DIFFRACTION95.36
2.92-3.350.17951520.18033007X-RAY DIFFRACTION94.81
3.35-4.220.16681590.14563020X-RAY DIFFRACTION94.47
4.22-65.140.17151520.15732940X-RAY DIFFRACTION93.05
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.903780385210.0543550588268-0.1103604894220.4289873583240.2586843085030.4124947065050.01481690599520.11143621754-0.303426275348-0.005988715206930.028542975928-0.01138521300020.02472813651990.0126437677033-0.04761872767910.1507918567610.0031207957636-0.02465210626180.0941717382483-0.007632886689450.160438204049-19.2346090963-27.43082219912.6959759879
24.5048570187-0.821871688043-0.3581307592716.295732369352.598648814462.13845403412-0.279720493174-1.203981338260.3563196087661.536767077250.1867185627420.2842849316320.638889967933-0.139032626140.07726737936110.5477054159860.02538762234420.01516604337610.5834047775230.03846402817930.346568811654-17.3819124096-27.082385157232.9434871766
32.06996153970.1539161778540.4698761628810.8936162378310.01824754800771.44690036771-0.0138457359561-0.2394600345590.1466722985370.0814332480392-0.00605145312993-0.0196596477438-0.0724177765386-0.0137058513140.03101038888070.1142337487410.017111310244-0.01196336933070.116105087969-0.02097386036580.108881088606-20.2200598348-15.38743306721.3919319545
42.19658485042-0.484581974261-0.5727664378750.572486833848-0.489099698970.8283543255860.0193527188086-0.1863907464740.0544679346616-0.0213101783630.00394522724832-0.0155354482184-0.00936238890786-0.0311565798636-0.03993637621480.19578237501-0.017829370277-0.007426180725780.1230834580010.02124279337980.174897851294-18.03332733392.309860604085.18888722188
52.48206079044-0.0460982691927-0.710347993321.167517399870.3003380240640.67846676344-0.1218791976260.100786641781-0.291978221257-0.02886719226930.0390675202638-0.01574822720340.0692668842841-0.009661569365830.06096938553870.1301715325810.0043616883253-0.0008752597780880.0956277719150.001328893060380.136610739371-11.4755186187-6.11799240587-2.79844493444
61.592476817210.1600103801740.3499599919980.9689488015710.3586303632410.948206188416-0.004476573651190.325163760103-0.0294308903441-0.189192342890.04831054066170.05924542684540.0552355575279-0.175434679168-0.005387584218020.132655895349-0.012308504226-0.007094826867320.1605172338910.01072720470240.0931669583099-12.65287145643.88617169438-10.969699477
73.58809664101-0.175516345720.1336329611732.023987253810.5729322933782.1769594276-0.0329077411040.3981937286630.445367247872-0.1390122127720.03419057461360.348336604573-0.0526468221737-0.154503757870.05945881920110.170625284225-0.0168149248135-0.01470460154770.1256760891040.02445138153620.153862804076-17.097969535714.5994541398-6.82027785598
82.243511809980.2571578495240.6889416195095.999712126240.6263523707131.72877659033-0.1163379564780.4903404261590.235666124386-0.2075750746480.1400942146880.102301918564-0.103350816831-0.395683224209-0.06735950260930.32093758602-0.0900737907096-0.09011896881870.4511466554930.08151424893530.293636422899-28.89950476118.87315606043-19.579101566
93.29326183625-0.07501461950190.8199514992530.726922903703-0.4407681520510.77285622771-0.105112299720.3642928658960.206711279167-0.1032060854560.0184379861778-0.143049416328-0.04333348127580.1497964199220.06575950757410.205683513083-0.03834572397460.007922657308290.202234244963-0.007588432783930.147777123364-7.834863579047.27197142693-10.5575092825
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 127 through 186 )BA127 - 1861 - 57
22chain 'B' and (resid 187 through 202 )BA187 - 20258 - 69
33chain 'B' and (resid 203 through 347 )BA203 - 34770 - 214
44chain 'A' and (resid 126 through 145 )AC126 - 1451 - 20
55chain 'A' and (resid 146 through 215 )AC146 - 21521 - 81
66chain 'A' and (resid 216 through 275 )AC216 - 27582 - 142
77chain 'A' and (resid 276 through 291 )AC276 - 291143 - 159
88chain 'A' and (resid 292 through 305 )AC292 - 305160 - 173
99chain 'A' and (resid 306 through 348 )AC306 - 348174 - 216

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