+Open data
-Basic information
Entry | Database: PDB / ID: 3dju | ||||||
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Title | Crystal structure of human BTG2 | ||||||
Components | Protein BTG2 | ||||||
Keywords | TRANSCRIPTION / helix-turn-helix / Transcription regulation | ||||||
Function / homology | Function and homology information dentate gyrus development / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / anterior/posterior pattern specification / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of neuroblast proliferation / central nervous system neuron development / skeletal muscle cell differentiation / associative learning / neuroblast proliferation / negative regulation of mitotic cell cycle ...dentate gyrus development / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / anterior/posterior pattern specification / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of neuroblast proliferation / central nervous system neuron development / skeletal muscle cell differentiation / associative learning / neuroblast proliferation / negative regulation of mitotic cell cycle / response to mechanical stimulus / response to electrical stimulus / response to organic cyclic compound / response to peptide hormone / neuron projection development / transcription corepressor activity / negative regulation of neuron apoptotic process / negative regulation of translation / negative regulation of cell population proliferation / DNA repair / DNA damage response / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Yang, X. / Morita, M. / Wang, H. / Suzuki, T. / Bartlam, M. / Yamamoto, T. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2008 Title: Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity Authors: Yang, X. / Morita, M. / Wang, H. / Suzuki, T. / Yang, W. / Luo, Y. / Zhao, C. / Yu, Y. / Bartlam, M. / Yamamoto, T. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dju.cif.gz | 37.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dju.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/3dju ftp://data.pdbj.org/pub/pdb/validation_reports/dj/3dju | HTTPS FTP |
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-Related structure data
Related structure data | 3djnC 2d5rS C: citing same article (ref.) 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: 13767.766 Da / Num. of mol.: 1 / Fragment: UNP residues 7-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTG2, B-cell translocation gene 2 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P78543 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.73 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 100mM BIS-TRIS, 0.2M Sodium chloride, 21% (v/v) PEG 3350, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. all: 5440 / Num. obs: 5309 / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D5R Resolution: 2.26→34.94 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.67 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.273 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.525 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→34.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.264→2.323 Å / Total num. of bins used: 20
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