[English] 日本語
![](img/lk-miru.gif)
- PDB-3gv6: Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 p... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gv6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide | ||||||
![]() |
| ||||||
![]() | Transcription/DNA binding protein / chromobox homolog / CBX6 / H3K9 peptide / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core / Transcription-DNA binding protein COMPLEX / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | ![]() PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / methylated histone binding / Regulation of PTEN gene transcription / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence ...PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / methylated histone binding / Regulation of PTEN gene transcription / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / nuclear body / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, A. / Amaya, M.F. / Li, Z. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Dong, A. / Amaya, M.F. / Li, Z. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Recognition and specificity determinants of the human cbx chromodomains. Authors: Kaustov, L. / Ouyang, H. / Amaya, M. / Lemak, A. / Nady, N. / Duan, S. / Wasney, G.A. / Li, Z. / Vedadi, M. / Schapira, M. / Min, J. / Arrowsmith, C.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 27.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 16.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 426.8 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2l11C ![]() 2l12C ![]() 2l1bC ![]() 3fdtC ![]() 3h91C ![]() 3i90C ![]() 3i91C ![]() 3dm1S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 7137.208 Da / Num. of mol.: 1 / Fragment: UNP residues 8-65 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Details: This sequence occurs naturally in Xenopus laevis / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 29.03 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 14% PEG 3350, 0.2M MgCl2, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 3, 2009 / Details: VeriMax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. all: 6339 / Num. obs: 6339 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.66 / Num. unique all: 547 / Rsym value: 0.473 / % possible all: 89.2 |
-
Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3DM1 Resolution: 1.76→24.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.142 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.219 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→24.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.76→1.807 Å / Total num. of bins used: 20
|