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- PDB-6tly: Crystal structure of the unconventional kinetochore protein Bodo ... -

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Basic information

Entry
Database: PDB / ID: 6tly
TitleCrystal structure of the unconventional kinetochore protein Bodo saltans KKT2 central domain
ComponentsProtein kinase, putative
KeywordsCELL CYCLE / kinetochore / zinc finger / kinetoplastid / KKT2
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
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
Protein kinase, putative
Similarity search - Component
Biological speciesBodo saltans (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsMarciano, G. / Nerusheva, O. / Ishii, M. / Akiyoshi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z United Kingdom
CitationJournal: 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.
History
DepositionDec 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6967
Polymers11,2721
Non-polymers4246
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-23 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.961, 53.512, 83.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-576-

GLY

21A-706-

CL

31A-837-

HOH

41A-893-

HOH

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Components

#1: Protein Protein kinase, putative


Mass: 11272.159 Da / Num. of mol.: 1 / Fragment: central domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bodo saltans (eukaryote) / Gene: BSAL_50690 / Plasmid: RSFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S4IKF4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40% PEG 400, 0.2 mM (NH4)2SO4, 100 mM Tris-HCL pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28297 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28297 Å / Relative weight: 1
ReflectionResolution: 1.8→45.02 Å / Num. obs: 8158 / % possible obs: 97.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.05 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
1.8-1.832.80.523340.780.3377.9
4.88-45.044.20.0724590.990.03597.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTER2.10.3 (3-OCT-2019)refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→35 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 403 4.94 %RANDOM
Rwork0.1948 ---
obs0.1963 8151 96.9 %-
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 32.04 Å2 / Biso min: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.0501 Å20 Å20 Å2
2--6.5119 Å20 Å2
3----6.4618 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 0 0 94 869
Biso mean---44.44 -
Num. residues----105
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d286SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes136HARMONIC5
X-RAY DIFFRACTIONt_it809HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion97SEMIHARMONIC5
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_contact719SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d809HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg1068HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion16.94
LS refinement shellResolution: 1.8→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2336 18 4.41 %
Rwork0.2423 390 -
all0.2419 408 -
obs--77.44 %

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