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Open data
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Basic information
Entry | Database: PDB / ID: 5vbc | ||||||
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Title | Crystal structure of ATXR5 in complex with histone H3.1 | ||||||
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![]() | TRANSFERASE/DNA BINDING PROTEIN / nucleosome / methylation / TRANSFERASE-DNA BINDING PROTEIN complex | ||||||
Function / homology | ![]() [histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / chromocenter / plastid / histone acetyltransferase activity / chloroplast / transcription coregulator activity / structural constituent of chromatin / nucleosome / methylation ...[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / chromocenter / plastid / histone acetyltransferase activity / chloroplast / transcription coregulator activity / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Couture, J.-F. / Bergamin, E. | ||||||
![]() | ![]() Title: Molecular basis for the methylation specificity of ATXR5 for histone H3. Authors: Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M.S. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.3 KB | Display | ![]() |
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PDB format | ![]() | 83.7 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 | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5va6C ![]() 5vabC ![]() 5vacC ![]() 5vahC ![]() 4o30S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26246.797 Da / Num. of mol.: 2 / Fragment: SET domain residues 146-374 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B9RU15, histone-lysine N-methyltransferase #2: Protein/peptide | Mass: 1345.590 Da / Num. of mol.: 2 / Fragment: residues 24-37 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 50% polypropylene glycol 400, 100mM Na-Hepes pH 6.0 and 5% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→27 Å / Num. obs: 29410 / % possible obs: 98.3 % / Redundancy: 4.1 % / Rsym value: 0.06 / Net I/σ(I): 12.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4o30 Resolution: 2.1→26.404 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.49 / Phase error: 26.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→26.404 Å
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Refine LS restraints |
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LS refinement shell |
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