+Open data
-Basic information
Entry | Database: PDB / ID: 7lga | ||||||
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Title | PEG10 CA-like C-terminal domain | ||||||
Components | Retrotransposon-derived protein PEG10 | ||||||
Keywords | ONCOPROTEIN / imprinted gene / domesticated Gag | ||||||
Function / homology | Function and homology information negative regulation of transforming growth factor beta receptor signaling pathway / cell differentiation / apoptotic process / DNA binding / RNA binding / zinc ion binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Zurowska, K. / Pornillos, O. / Ganser-Pornillos, B.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2022 Title: Structural evidence that MOAP1 and PEG10 are derived from retrovirus/retrotransposon Gag proteins. Authors: Zurowska, K. / Alam, A. / Ganser-Pornillos, B.K. / Pornillos, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lga.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lga.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 7lga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lga_validation.pdf.gz | 446.4 KB | Display | wwPDB validaton report |
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Full document | 7lga_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 7lga_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7lga_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/7lga ftp://data.pdbj.org/pub/pdb/validation_reports/lg/7lga | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11701.937 Da / Num. of mol.: 4 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Details: The first 9 amino acids (GHHHHHHGS) is a purification tag derived from the expression vector. Source: (gene. exp.) Homo sapiens (human) / Gene: PEG10, EDR, KIAA1051, MAR2, MART2, MEF3L1, RGAG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q86TG7 #2: 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: 2.04 Å3/Da / Density % sol: 39.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5 25% (w/v) PEG 3,350 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 58024 / % possible obs: 98.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.19 Å2 / CC1/2: 0.992 / Net I/σ(I): 19.625 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 1166 / CC1/2: 0.644 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→41.89 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.4287 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 25.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.89 Å
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Refine LS restraints |
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LS refinement shell |
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