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- PDB-8fjn: Crystal Structure of the Trypanosoma brucei DOT1A histone H3K76 m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fjn | ||||||
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Title | Crystal Structure of the Trypanosoma brucei DOT1A histone H3K76 methyltransferase in complex with AdoHcy - C2221 space group | ||||||
![]() | Histone-lysine N-methyltransferase, H3 lysine-79 specific | ||||||
![]() | TRANSFERASE / HISTONE LYSINE METHYLTRANSFERASE / Histone-modifying enzyme / DOT1A / Trypanosoma brucei / AdoHcy complex | ||||||
Function / homology | ![]() histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / DNA damage checkpoint signaling / chromosome / methylation / DNA repair / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Frisbie, V.S. / Hashimoto, H. / Debler, E.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Mechanism of the atypical Trypanosoma brucei DOT1A histone H3K76 methyltransferase Authors: Frisbie, V.S. / Hashimoto, H. / Xie, Y. / Baeza, J. / Nguyen, T. / Yuan, Z. / Garcia, B.A. / Debler, E.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fjmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29325.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q581Z0, [histone H3]-lysine79 N-trimethyltransferase |
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-Non-polymers , 5 types, 134 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAH / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 30% (w/v) PEG 8,000, 200 mM calcium acetate, 100 mM MES-NaOH, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42.49 Å / Num. obs: 16832 / % possible obs: 95.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 26.76 Å2 / CC1/2: 0.967 / CC star: 0.992 / Rpim(I) all: 0.058 / Rsym value: 0.109 / Χ2: 0.957 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.4 % / Num. unique obs: 1354 / CC1/2: 0.863 / CC star: 0.962 / Rpim(I) all: 0.372 / Rsym value: 0.566 / Χ2: 0.991 / % possible all: 78.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→42.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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