+
Open data
-
Basic information
Entry | Database: PDB / ID: 4gur | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LSD2-NPAC with H3 in space group P21 | ||||||
![]() |
| ||||||
![]() | ![]() | ||||||
Function / homology | ![]() DNA methylation involved in gamete generation / negative regulation of chromosome condensation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, F. / Dong, Z. / Fang, J. / Yang, Y. / Li, Z. / Xu, Y. / Yang, H. / Wang, P. / Fang, R. / Shi, Y. / Xu, Y. | ||||||
![]() | ![]() Title: LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / ...Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / Zhou, Q. / Li, J. / Marynick, M.P. / Li, X. / Lu, H. / Kaiser, U.B. / Kingston, R.E. / Xu, Y. / Shi, Y.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 169.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 562.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 578.2 KB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gu1SC ![]() 4gusC ![]() 4gutC ![]() 4guuC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 87051.547 Da / Num. of mol.: 1 / Fragment: UNP residues 51-822 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 13528.271 Da / Num. of mol.: 1 / Fragment: UNP residues 152-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | ![]() Mass: 2263.666 Da / Num. of mol.: 1 / Fragment: UNP residues 2-22 / Mutation: K4M / Source method: obtained synthetically / Details: H3K4 is mutated to Met / Source: (synth.) ![]() ![]() |
---|
-Non-polymers , 4 types, 103 molecules 






#4: Chemical | ChemComp-FAD / ![]() | ||
---|---|---|---|
#5: Chemical | ChemComp-GOL / ![]() | ||
#6: Chemical | #7: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.16 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2010 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 28816 / % possible obs: 88.57 % / Biso Wilson estimate: 39.29 Å2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 4GU1 Resolution: 2.506→38.867 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8426 / SU ML: 0.3 / σ(F): 0.06 / Phase error: 22.9 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.285 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.21 Å2 / Biso mean: 51.6845 Å2 / Biso min: 19.21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.506→38.867 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
|