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- PDB-2r3a: Methyltransferase domain of human suppressor of variegation 3-9 h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r3a | ||||||
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Title | Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 | ||||||
![]() | Histone-lysine N-methyltransferase SUV39H2 | ||||||
![]() | TRANSFERASE / Histone H3-K9 methyltransferase 2 / Histone-lysine N-methyltransferase / H3 lysine-9 specific 2 / Alternative splicing / Cell cycle / Chromatin regulator / Chromosomal protein / Differentiation / Nucleus / Repressor / S-adenosyl-L-methionine / Telomere / Transcription / Transcription regulation / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() [histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 methyltransferase activity / epigenetic programming in the zygotic pronuclei / S-adenosyl-L-methionine binding / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / chromosome, centromeric region / ubiquitin-like ligase-substrate adaptor activity / PKMTs methylate histone lysines ...[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / histone H3K9 methyltransferase activity / epigenetic programming in the zygotic pronuclei / S-adenosyl-L-methionine binding / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / chromosome, centromeric region / ubiquitin-like ligase-substrate adaptor activity / PKMTs methylate histone lysines / circadian rhythm / chromatin organization / cellular response to hypoxia / methylation / cell differentiation / transcription cis-regulatory region binding / chromatin remodeling / cell cycle / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lunin, V.V. / Wu, H. / Zeng, H. / Ren, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Lunin, V.V. / Wu, H. / Zeng, H. / Ren, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural biology of human H3K9 methyltransferases Authors: Wu, H. / Min, J. / Lunin, V.V. / Antoshenko, T. / Dombrovski, L. / Zeng, H. / Allali-Hassani, A. / Campagna-Slater, V. / Vedadi, M. / Arrowsmith, C.H. / Plotnikov, A.N. / Schapira, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 805 KB | Display | ![]() |
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Full document | ![]() | 807.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2igqC ![]() 2o8jC ![]() 2qpwC ![]() 2rfiC ![]() 3hnaC ![]() 1mhv S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33980.547 Da / Num. of mol.: 1 / Fragment: Methyltransferase domain: Residues 112-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9H5I1, histone-lysine N-methyltransferase | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAM / | #4: Chemical | ChemComp-SER / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 10000, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 22956 / Num. obs: 22956 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.084 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2190 / Rsym value: 0.336 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1MHV ![]() 1mhv Resolution: 2→35.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.647 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.989 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.055 Å / Total num. of bins used: 20
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