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- PDB-6tlx: Crystal structure of the unconventional kinetochore protein Perki... -

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Basic information

Entry
Database: PDB / ID: 6tlx
TitleCrystal structure of the unconventional kinetochore protein Perkinsela sp. KKT2a central domain
ComponentsProtein kinase
KeywordsCELL CYCLE / kinetochore / zinc finger / kinetoplastid / KKT2
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesPerkinsela sp. CCAP 1560/4 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.87 Å
AuthorsMarciano, G. / Nerusheva, O. / Ishii, M. / Akiyoshi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z United Kingdom
Citation
Journal: J.Cell Biol. / Year: 2021
Title: Kinetoplastid kinetochore proteins KKT2 and KKT3 have unique centromere localization domains.
Authors: Marciano, G. / Ishii, M. / Nerusheva, O.O. / Akiyoshi, B.
#1: Journal: Biorxiv / Year: 2019
Title: Unconventional kinetochore kinases KKT2 and KKT3 have a unique zinc finger that promotes their kinetochore localization
Authors: Marciano, G. / Nerusheva, O. / Ishii, M. / Akiyoshi, B.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7013
Polymers14,5711
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7870 Å2
Unit cell
Length a, b, c (Å)113.845, 113.845, 46.013
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Protein kinase /


Mass: 14570.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Perkinsela sp. CCAP 1560/4 (eukaryote) / Gene: XU18_4017 / Plasmid: RSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L1KLX8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 5.91 Å3/Da / Density % sol: 79.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 19% MPD, 50 mM Hepes, pH 7.5, 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.87→56.92 Å / Num. obs: 7986 / % possible obs: 99.7 % / Redundancy: 19.2 % / Biso Wilson estimate: 105.112 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.024 / Rrim(I) all: 0.105 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.87-2.9219.51.0452.13570.450.2491.8
7.77-56.9316.10.04860.54320.99100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
DIALS1.8.4data reduction
CRANK2phasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.87→49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.259
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 377 4.84 %RANDOM
Rwork0.2529 ---
obs0.2538 7785 97.2 %-
Displacement parametersBiso max: 163.08 Å2 / Biso mean: 113.37 Å2 / Biso min: 87.09 Å2
Baniso -1Baniso -2Baniso -3
1--8.0282 Å20 Å20 Å2
2---8.0282 Å20 Å2
3---16.0563 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: final / Resolution: 2.87→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 2 0 834
Biso mean--100.6 --
Num. residues----112
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d271SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes147HARMONIC5
X-RAY DIFFRACTIONt_it854HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion116SEMIHARMONIC5
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_contact632SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d854HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1161HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion17.8
LS refinement shellResolution: 2.87→3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.5116 16 3.7 %
Rwork0.3663 417 -
all0.3719 433 -
obs--86.83 %

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