+Open data
-Basic information
Entry | Database: PDB / ID: 7mto | ||||||||||||
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Title | Crystal Structure of SET/I2PP2A/TAF-1Beta core | ||||||||||||
Components | Isoform 2 of Protein SET | ||||||||||||
Keywords | ONCOPROTEIN / Inhibitor of PP2A / ceramide binding / nucleosome assembly protein (NAP) domain | ||||||||||||
Function / homology | Function and homology information HuR (ELAVL1) binds and stabilizes mRNA / protein phosphatase regulator activity / nucleosome disassembly / protein phosphatase inhibitor activity / lipid droplet / Condensation of Prophase Chromosomes / nucleosome assembly / histone binding / DNA replication / negative regulation of neuron apoptotic process ...HuR (ELAVL1) binds and stabilizes mRNA / protein phosphatase regulator activity / nucleosome disassembly / protein phosphatase inhibitor activity / lipid droplet / Condensation of Prophase Chromosomes / nucleosome assembly / histone binding / DNA replication / negative regulation of neuron apoptotic process / negative regulation of DNA-templated transcription / chromatin binding / chromatin / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.791 Å | ||||||||||||
Authors | Roth, B.M. / DePalma, R.M. / Ogretmen, B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal Structure of SET/I2PP2A/TAF-1Beta core Authors: Roth, B.M. / DePalma, R.M. / Ogretmen, B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mto.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mto.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mto_validation.pdf.gz | 422.3 KB | Display | wwPDB validaton report |
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Full document | 7mto_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 7mto_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 7mto_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/7mto ftp://data.pdbj.org/pub/pdb/validation_reports/mt/7mto | HTTPS FTP |
-Related structure data
Related structure data | 2e50S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24056.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SET / Variant: Isoform 2 / Plasmid: pET28a(+)_TEV_NdCdSET-WT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01105 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 0.1 M Imidazole, 0.2M calcium acetate, 22% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.791→50 Å / Num. obs: 22528 / % possible obs: 97.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.029 / Rrim(I) all: 0.059 / Χ2: 1.027 / Net I/σ(I): 10.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+50 / Resolution: 1.791→38.521 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.69 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.53 Å2 / Biso mean: 32.9437 Å2 / Biso min: 13.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.791→38.521 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 5.3988 Å / Origin y: -16.8283 Å / Origin z: -24.5914 Å
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Refinement TLS group |
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