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- PDB-6zpk: Crystal structure of the unconventional kinetochore protein Trypa... -

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Basic information

Entry
Database: PDB / ID: 6zpk
TitleCrystal structure of the unconventional kinetochore protein Trypanosoma brucei KKT4 BRCT domain
ComponentsTrypanosoma brucei KKT4 463-645
KeywordsCELL CYCLE / kinetochore / kinetoplastid / KKT4 / BRCT
Function / homologySMC5-SMC6 complex localization factor protein 1 / positive regulation of double-strand break repair / BRCT domain superfamily / spindle microtubule / chromosome segregation / kinetochore / microtubule binding / nucleus / BRCT domain-containing protein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.57 Å
AuthorsLudzia, P. / Lowe, E.D. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210622/Z/18/Z United Kingdom
Citation
Journal: Structure / Year: 2021
Title: Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein.
Authors: Ludzia, P. / Lowe, E.D. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B.
#1: Journal: Biorxiv / Year: 2020
Title: Structural characterisation of KKT4, an unconventional microtubule-binding kinetochore protein
Authors: Ludzia, P. / Lowe, E. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypanosoma brucei KKT4 463-645
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3193
Polymers20,1311
Non-polymers1882
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS analysis revealed that KKT4 463-645 is a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-12 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.368, 61.633, 67.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Trypanosoma brucei KKT4 463-645 / Trypanosoma brucei KKT4 463-645


Mass: 20130.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Highlighted residues are not visible in the electron density. Trypanosoma brucei KKT4 463-645
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.8.3680 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q580Y8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: HEPES, sodium chloride, bis-Tris, ammonium sulphate, TCEP

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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: 1.56956→45.6013 Å / Num. obs: 27084 / % possible obs: 97.3 % / Redundancy: 10 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.997 / Net I/σ(I): 14
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.549 / Num. unique obs: 1025 / CC1/2: 0.496 / Rpim(I) all: 0.319 / Rrim(I) all: 0.641

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
DIALSdata scaling
BUCCANEERmodel building
Arcimboldophasing
DIALSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.57→45.6 Å / SU ML: 0.1434 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1667 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1922 1322 4.91 %
Rwork0.1732 25623 -
obs0.1741 26945 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.04 Å2
Refinement stepCycle: LAST / Resolution: 1.57→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 11 205 1448

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