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- PDB-8a0j: Crystal structure of the kinetoplastid kinetochore protein Trypan... -

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Basic information

Entry
Database: PDB / ID: 8a0j
TitleCrystal structure of the kinetoplastid kinetochore protein Trypanosoma congolense KKT2 divergent polo-box domain
ComponentsUncharacterized protein TCIL3000_11_11110
KeywordsCELL CYCLE / kinetochore / polo-box / kinetoplastid / KKT2
Function / homology
Function and homology information


polo kinase / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
POLO box domain / POLO box domain profile. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...POLO box domain / POLO box domain profile. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesTrypanosoma congolense IL3000 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsIshii, M. / Ludzia, P. / Marciano, G. / Allen, W. / Nerusheva, O. / Akiyoshi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z United Kingdom
Citation
Journal: Mol.Biol.Cell / Year: 2022
Title: Divergent polo boxes in KKT2 bind KKT1 to initiate the kinetochore assembly cascade in Trypanosoma brucei.
Authors: Ishii, M. / Ludzia, P. / Marciano, G. / Allen, W. / Nerusheva, O.O. / Akiyoshi, B.
#1: Journal: Biorxiv / Year: 2022
Title: Divergent polo boxes in KKT2 and KKT3 initiate the kinetochore assembly cascade in Trypanosoma brucei
Authors: Ishii, M. / Ludzia, P. / Marciano, G. / Allen, W. / Nerusheva, O.O. / Akiyoshi, B.
History
DepositionMay 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein TCIL3000_11_11110
B: Uncharacterized protein TCIL3000_11_11110


Theoretical massNumber of molelcules
Total (without water)53,8992
Polymers53,8992
Non-polymers00
Water3,333185
1
A: Uncharacterized protein TCIL3000_11_11110


Theoretical massNumber of molelcules
Total (without water)26,9501
Polymers26,9501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein TCIL3000_11_11110


Theoretical massNumber of molelcules
Total (without water)26,9501
Polymers26,9501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.700, 57.133, 83.671
Angle α, β, γ (deg.)90.000, 97.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein TCIL3000_11_11110


Mass: 26949.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma congolense IL3000 (eukaryote)
Strain: IL3000 / Gene: TCIL3000_11_11110 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0V1V5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 8% w/v Polyvinyl alcohol, 10% v/v 1-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.921→48.26 Å / Num. obs: 33539 / % possible obs: 95.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 12.3
Reflection shellResolution: 1.921→1.954 Å / Num. unique obs: 1736 / CC1/2: 0.404

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSFeb 5, 2021data reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 2.2→48.24 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 1138 4.88 %
Rwork0.1942 22162 -
obs0.1968 23300 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.64 Å2 / Biso mean: 40.9715 Å2 / Biso min: 19.34 Å2
Refinement stepCycle: final / Resolution: 2.2→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 0 185 3674
Biso mean---40.68 -
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.30.29681540.269527212875
2.3-2.420.28351290.221727482877
2.42-2.570.25271550.224527552910
2.57-2.770.25591310.211127452876
2.77-3.050.2691270.2127962923
3.05-3.490.26971390.196127782917
3.49-4.40.23951450.166427952940
4.4-48.240.20691580.176428242982
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)
14.6421-0.348-0.64774.55640.05024.44780.4812-0.3260.22910.1221-0.06310.2195-0.2633-0.2872-0.2010.3415-0.0065-0.03550.161-0.00320.2023-4.0932-5.25069.836
21.3817-0.06130.24083.4979-0.34462.1198-0.0015-0.10690.04070.1669-0.0512-0.1404-0.17120.11040.03530.281-0.0266-0.00220.20670.01050.28856.57826.81867.02
30.96870.7656-0.57392.19880.97822.9137-0.0821-0.03050.0097-0.1264-0.04170.1799-0.0399-0.10040.09920.28140.0305-0.01840.17790.00870.2542-0.5016-5.83959.5352
43.9956-0.01131.67052.2802-1.19014.10660.2156-0.5-0.07920.3983-0.10210.07040.14540.0229-0.06420.38920.0130.06140.23050.01530.225-1.9136-13.450420.9132
52.4395-0.4619-0.76724.36750.53034.6988-0.0678-0.00990.28770.0672-0.50380.24920.7353-0.65410.39680.20720.0040.00350.4164-0.04140.271-24.48220.5936.3996
62.33150.4328-1.52443.33750.96994.51530.0509-0.0406-0.349-0.0376-0.1553-0.19820.37550.27340.07970.24520.0299-0.01260.32750.02070.2429-15.483210.49137.6775
71.999-0.70810.46252.66620.20122.9122-0.1732-0.0688-0.34230.46040.11910.19910.4241-0.1540.11420.536-0.05560.04570.33660.00080.3143-24.13059.25849.635
81.865-0.5996-0.61113.1633-0.03812.32910.14140.22110.0185-0.1413-0.15950.1769-0.2068-0.25210.03680.2530.03230.01740.3665-0.02150.2148-23.998821.955534.6841
92.8012-0.53420.06563.9183-0.11251.6463-0.01560.69620.0729-0.8422-0.1172-0.05440.0354-0.07760.12180.54590.10860.00740.68070.05080.2911-21.163526.219422.1809
104.5909-0.55571.52644.2744-0.86586.4396-0.05410.31411.39570.2084-0.3773-0.3163-1.13360.24070.32850.4529-0.05240.12750.33180.0730.3492-12.769135.05529.8238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1039 through 1065 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1066 through 1159 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1160 through 1222 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1223 through 1261 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1046 through 1065 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1066 through 1127 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1128 through 1158 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1159 through 1222 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1223 through 1244 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1245 through 1262 )B0

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