[English] 日本語
![](img/lk-miru.gif)
- PDB-6zpm: Crystal structure of the unconventional kinetochore protein Trypa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6zpm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the unconventional kinetochore protein Trypanosoma cruzi KKT4 coiled coil domain | ||||||
![]() | Trypanosoma cruzi KKT4 117-218 | ||||||
![]() | CELL CYCLE / KKT4 / kinetochore / kinetoplastids / microtubules | ||||||
Function / homology | BRCT domain superfamily / THREONINE / Putative kinetoplastid kinetochore protein 4![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ludzia, P. / Lowe, D.E. / Marciano, G. / Mohammed, S. / Redfield, C. / Akiyoshi, B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 328.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 330.1 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
Components
#1: Protein | Mass: 12437.032 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal residue Gly is not visible in the electron density. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-THR / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.03 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: HEPES, sodium chloride, MOPSO, Bis-Tris, DL-Arginine hydrochloride, DL- Threonine, DL-Histidine monohydrochloride monohydrate, DL-5-Hydroxylysine hydrochloride, trans-4-hydroxy-L-proline, ...Details: HEPES, sodium chloride, MOPSO, Bis-Tris, DL-Arginine hydrochloride, DL- Threonine, DL-Histidine monohydrochloride monohydrate, DL-5-Hydroxylysine hydrochloride, trans-4-hydroxy-L-proline, PEG 8000, 1,5- Pentanediol, TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→67.96 Å / Num. obs: 16787 / % possible obs: 90.36 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.04 / Rrim(I) all: 0.103 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.9→3.88 Å / Num. unique obs: 1452 / CC1/2: 0.274 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.9→67.96 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.83 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.44 Å2 / Biso mean: 37.1107 Å2 / Biso min: 8.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→67.96 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|