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Yorodumi- PDB-6luk: Crystal structure of the SAMD1 SAM domain in another crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6luk | |||||||||
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Title | Crystal structure of the SAMD1 SAM domain in another crystal form | |||||||||
Components | Atherin | |||||||||
Keywords | DNA BINDING PROTEIN / CpG-islands / transcription / decamer | |||||||||
Function / homology | Function and homology information lipoprotein lipid oxidation / foam cell differentiation / low-density lipoprotein particle binding / : / protein homooligomerization / chromatin organization / chromosome / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding ...lipoprotein lipid oxidation / foam cell differentiation / low-density lipoprotein particle binding / : / protein homooligomerization / chromatin organization / chromosome / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular space / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.054 Å | |||||||||
Authors | Cao, Y. / Zhou, Y. / Wang, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: Sci Adv / Year: 2021 Title: The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. Authors: Stielow, B. / Zhou, Y. / Cao, Y. / Simon, C. / Pogoda, H.M. / Jiang, J. / Ren, Y. / Phanor, S.K. / Rohner, I. / Nist, A. / Stiewe, T. / Hammerschmidt, M. / Shi, Y. / Bulyk, M.L. / Wang, Z. / Liefke, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6luk.cif.gz | 290.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6luk.ent.gz | 238.3 KB | Display | PDB format |
PDBx/mmJSON format | 6luk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6luk_validation.pdf.gz | 524.5 KB | Display | wwPDB validaton report |
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Full document | 6luk_full_validation.pdf.gz | 531.7 KB | Display | |
Data in XML | 6luk_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 6luk_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6luk ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6luk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 7810.881 Da / Num. of mol.: 20 / Fragment: SAM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMD1 / Production host: Escherichia Coli BL21(DE3) (bacteria) / References: UniProt: Q6SPF0 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.6 Å3/Da / Density % sol: 52.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1M bis-tris (pH 7.5), 2.1M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 2.054→50 Å / Num. obs: 98440 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.054→2.12 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8178 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A model solved by Se-Met labelled sample. Resolution: 2.054→45.71 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.84 Å2 / Biso mean: 27.0811 Å2 / Biso min: 13.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.054→45.71 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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