+
Open data
-
Basic information
Entry | Database: PDB / ID: 6k5u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the myb domain of S. pombe Tbf1 | ||||||
![]() | Telomeric DNA-binding factor trf1 | ||||||
![]() | DNA BINDING PROTEIN / Telomere binding protein | ||||||
Function / homology | ![]() chromosome, telomeric repeat region / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / cell cycle / telomere maintenance / chromatin / protein homodimerization activity / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, Y.Z. / Wang, N.N. / Zhao, Y.C. / Zeng, Z.X. | ||||||
![]() | ![]() Title: Crystal structure of the myb domain of S. pombe Tbf1 Authors: Zhou, Y.Z. / Wang, N.N. / Zhao, Y.C. / Zeng, Z.X. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 42.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 32.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 9116.227 Da / Num. of mol.: 2 / Mutation: L420M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: trf1, SPBC19G7.13 / Variant: 972 / ATCC 24843 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | L420M is mutated and MET is modified to MSE. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % |
---|---|
Crystal grow | Temperature: 277.15 K / Method: vapor diffusion Details: 16% PEG 8000, 40mM Potassium phosphate dibasic, 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 2.079→40 Å / Num. obs: 14514 / % possible obs: 100 % / Redundancy: 24.7 % / Biso Wilson estimate: 26.39 Å2 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.038 / Rrim(I) all: 0.189 / Χ2: 1.368 / Net I/σ(I): 32.455 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 23.4 % / Rmerge(I) obs: 0.873 / Num. unique obs: 696 / CC1/2: 0.964 / Rpim(I) all: 0.183 / Rrim(I) all: 0.893 / Χ2: 0.494 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.07 Å2 / Biso mean: 29.0306 Å2 / Biso min: 13.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.079→37.262 Å
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
|