+Open data
-Basic information
Entry | Database: PDB / ID: 3dal | ||||||
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Title | Methyltransferase domain of human PR domain-containing protein 1 | ||||||
Components | PR domain zinc finger protein 1 | ||||||
Keywords | TRANSFERASE / Methyltransferase / PRDM1 / Structural Genomics / Structural Genomics Consortium / SGC / DNA-binding / Metal-binding / Nucleus / Polymorphism / Repressor / Transcription / Transcription regulation / Zinc / Zinc-finger / DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information regulation of extrathymic T cell differentiation / regulation of NK T cell differentiation / sebum secreting cell proliferation / regulation of natural killer cell differentiation / morphogenesis of a branching structure / maternal placenta development / trophoblast giant cell differentiation / eye photoreceptor cell development / intestinal epithelial cell development / heart valve development ...regulation of extrathymic T cell differentiation / regulation of NK T cell differentiation / sebum secreting cell proliferation / regulation of natural killer cell differentiation / morphogenesis of a branching structure / maternal placenta development / trophoblast giant cell differentiation / eye photoreceptor cell development / intestinal epithelial cell development / heart valve development / coronary vasculature development / Regulation of TP53 Expression / aorta development / artery morphogenesis / ventricular septum development / germ cell development / cell fate commitment / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / methyltransferase activity / kidney development / promoter-specific chromatin binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / methylation / regulation of gene expression / adaptive immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å | ||||||
Authors | Amaya, M.F. / Zeng, H. / Antoshenko, T. / Dong, A. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Amaya, M.F. / Zeng, H. / Antoshenko, T. / Dong, A. / Loppnau, P. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of methyltransferase domain of human PR domain-containing protein 1 Authors: Zeng, H. / Amaya, M.F. / Antoshenko, T. / Dong, A. / Loppnau, P. / Bochkarev, A. / Min, J. / Plotnikov, A.N. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dal.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dal.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dal ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dal | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22692.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM1, BLIMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75626 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Purified PRDM1 was crystallized using hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 2.0 M Na Formide, 0. ...Details: Purified PRDM1 was crystallized using hanging drop vapor diffusion method at 20 C by mixing 1.5 l of the protein solution with 1.5 l of the reservoir solution containing 2.0 M Na Formide, 0.1 M sodium acetate, pH 4.6., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28268 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.28268 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 57924 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.061 / Χ2: 1.197 / Net I/σ(I): 10.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.764 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 22.253 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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