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- PDB-6zpj: Crystal structure of the unconventional kinetochore protein Leish... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zpj | ||||||
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Title | Crystal structure of the unconventional kinetochore protein Leishmania mexicana KKT4 coiled coil domain | ||||||
![]() | Leishmania mexicana KKT4 | ||||||
![]() | CELL CYCLE / kinetochore / kinetoplastid / microtubules / coiled coil | ||||||
Function / homology | BRCT domain superfamily / IMIDAZOLE / 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 | ![]() | 108.4 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 341.3 KB | Display | ![]() |
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Full document | ![]() | 342.3 KB | Display | |
Data in XML | ![]() | 12.7 KB | Display | |
Data in CIF | ![]() | 18.4 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: 14416.385 Da / Num. of mol.: 2 / Mutation: R218Q Source method: isolated from a genetically manipulated source Details: Expressed protein contains an additional 23 residues from the expression vector at its C-terminus due to a cloning error, which failed to place a stop codon after the KKT4 coding sequence. ...Details: Expressed protein contains an additional 23 residues from the expression vector at its C-terminus due to a cloning error, which failed to place a stop codon after the KKT4 coding sequence. Only 7 out of 23 residues were visible in the electron density. Source: (gene. exp.) ![]() Gene: LMXM_10_0300 / Plasmid: pRSFDuet-1 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES, sodium chloride, imidazole, MPD, 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: Jul 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→61.1511 Å / Num. obs: 22522 / % possible obs: 98.34 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.9→4.322 Å / Num. unique obs: 1840 / CC1/2: 0.352 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.9→61.15 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.9208 / 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: 30.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→61.15 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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