+
Open data
-
Basic information
Entry | Database: PDB / ID: 5lph | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the TOG domain of human Cep104 | ||||||
![]() | Centrosomal protein of 104 kDa | ||||||
![]() | CELL CYCLE / TOG domain / HEAT repeat / Tubulin binding / Cep104 / Basal body / Centriole / Cilia | ||||||
Function / homology | ![]() thienylcyclohexylpiperidine binding / glutamate binding / glycine binding / centriole / cilium / spindle pole / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | van Breugel, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase. Authors: Al-Jassar, C. / Andreeva, A. / Barnabas, D.D. / McLaughlin, S.H. / Johnson, C.M. / Yu, M. / van Breugel, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 92.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-
Components
#1: Protein | Mass: 32590.248 Da / Num. of mol.: 2 / Fragment: TOG domain, UNP residues 392-676 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.58 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0 11 % PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2014 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→49.5 Å / Num. obs: 40229 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.667 / % possible all: 99.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.25→49.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|