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- PDB-8a0k: crystal structure of the kinetoplastid kinetochore protein Trypan... -

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Basic information

Entry
Database: PDB / ID: 8a0k
Titlecrystal structure of the kinetoplastid kinetochore protein Trypanosoma brucei KKT3 Divergent Polo-Box domain
ComponentsProtein kinase, putative
KeywordsCELL CYCLE / polo-box / Kinetochore / KKT3 / Kinetoplastid
Function / homology
Function and homology information


polo kinase / chromosome segregation / kinetochore / protein phosphorylation / intracellular signal transduction / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
: / POLO box domain / POLO box domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / 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 ...: / POLO box domain / POLO box domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / 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
DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase PLK
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.92 Å
AuthorsIshii, M. / Ludzia, P. / Marciano, G. / Allen, W. / Nerusheva, O.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: Protein kinase, putative
B: Protein kinase, putative
C: Protein kinase, putative
D: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6076
Polymers98,3954
Non-polymers2122
Water90150
1
A: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7052
Polymers24,5991
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7052
Polymers24,5991
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein kinase, putative


Theoretical massNumber of molelcules
Total (without water)24,5991
Polymers24,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein kinase, putative


Theoretical massNumber of molelcules
Total (without water)24,5991
Polymers24,5991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.998, 52.485, 102.152
Angle α, β, γ (deg.)84.110, 84.420, 73.250
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein kinase, putative


Mass: 24598.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb09.211.2260 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q38DT1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1 M Bis-Tris pH 5.5 and 0.1 M tri-sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.0072 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0072 Å / Relative weight: 1
ReflectionResolution: 2.92→50.68 Å / Num. obs: 19067 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 63.19 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.098 / Rrim(I) all: 0.184 / Net I/σ(I): 5.1 / Num. measured all: 65155 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.92-31.022475613820.530.6431.2131.498.4
13.06-50.680.1067312120.9680.0660.12510.199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.92 Å50.68 Å
Translation2.92 Å50.68 Å

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimless0.5.26data scaling
PHASER2.8.3phasing
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: partial Se-Met model

Resolution: 2.92→50.68 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.433
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 952 5.01 %RANDOM
Rwork0.2504 ---
obs0.2515 18988 98.6 %-
Displacement parametersBiso max: 163.6 Å2 / Biso mean: 81.54 Å2 / Biso min: 26 Å2
Baniso -1Baniso -2Baniso -3
1-6.7368 Å2-8.0496 Å2-3.4721 Å2
2--1.8403 Å2-23.9987 Å2
3----8.577 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 2.92→50.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6169 0 14 50 6233
Biso mean--95.75 49.47 -
Num. residues----815
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1991SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1074HARMONIC5
X-RAY DIFFRACTIONt_it6344HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion815SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4463SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6364HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8687HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion18.98
LS refinement shellResolution: 2.92→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 48
RfactorNum. reflection% reflection
Rfree0.4716 21 5.2 %
Rwork0.3512 383 -
all0.3563 404 -
obs--96.45 %
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)
111.24682.30413.75316.0589-0.43686.0839-0.3902-0.52910.36240.17660.2090.2349-0.0576-0.12680.1812-0.37130.02390.0941-0.3071-0.0472-0.094441.6684-22.99188.4225
24.57530.284-0.205110.7942-4.200310.5965-0.0441-0.1455-0.0175-0.5466-0.3530.10890.7711-0.07280.3971-0.05390.1226-0.00550.2106-0.0121-0.185524.5723-1.620834.0761
39.0955-5.7531-0.44811.8544-1.78524.4136-0.04610.53840.3997-0.4899-0.074-0.92650.09070.20950.1201-0.3851-0.13040.002-0.285-0.0216-0.221751.8316-3.2223-11.9278
45.9533-0.5023-1.33857.7011-3.834211.91680.20990.4188-0.3199-0.9581-0.6425-0.77080.91380.5480.4326-0.23670.04230.0207-0.13480.1997-0.217235.2106-23.365258.9538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 210
2X-RAY DIFFRACTION2{ B|* }B0 - 209
3X-RAY DIFFRACTION3{ C|* }C2 - 211
4X-RAY DIFFRACTION4{ D|* }D0 - 209

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