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- PDB-5t0m: A histone H3K9M mutation traps histone methyltransferase Clr4 to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5t0m | |||||||||||||||
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Title | A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading | |||||||||||||||
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Function / homology | ![]() regulation of protein modification process / histone H3K56 methyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Xu, K. / Tong, L. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. Authors: Shan, C.M. / Wang, J. / Xu, K. / Chen, H. / Yue, J.X. / Andrews, S. / Moresco, J.J. / Yates, J.R. / Nagy, P.L. / Tong, L. / Jia, S. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.7 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5t0kC ![]() 2o8jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABPC
#1: Protein | Mass: 32460.799 Da / Num. of mol.: 2 / Fragment: unp residues 879-1159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q96KQ7, ![]() ![]() #2: Protein/peptide | Mass: 1549.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 363 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ![]() #5: Chemical | ChemComp-SAH / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→50 Å / Num. obs: 49342 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 5.8 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2O8J Resolution: 1.896→44.897 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.896→44.897 Å
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Refine LS restraints |
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LS refinement shell |
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