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- PDB-6zpk: Crystal structure of the unconventional kinetochore protein Trypa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zpk | ||||||
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Title | Crystal structure of the unconventional kinetochore protein Trypanosoma brucei KKT4 BRCT domain | ||||||
![]() | Trypanosoma brucei KKT4 463-645 | ||||||
![]() | CELL CYCLE / kinetochore / kinetoplastid / KKT4 / BRCT | ||||||
Function / homology | BRCT domain superfamily / chromosome segregation / spindle microtubule / kinetochore / microtubule binding / nucleus / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ludzia, P. / Lowe, E.D. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
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PDB format | ![]() | 64.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 318.2 KB | Display | ![]() |
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Full document | ![]() | 318.2 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.8.3680 / Plasmid: pNIC28-Bsa4 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: HEPES, sodium chloride, bis-Tris, ammonium sulphate, TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||
Displacement parameters | Biso mean: 23.04 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→45.6 Å
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