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Yorodumi- PDB-2g3r: Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g3r | ||||||
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Title | Crystal Structure of 53BP1 tandem tudor domains at 1.2 A resolution | ||||||
Components | Tumor suppressor p53-binding protein 1 | ||||||
Keywords | CELL CYCLE/TRANSCRIPTION / TANDEM TUDOR DOMAINS / CELL CYCLE-TRANSCRIPTION COMPLEX | ||||||
Function / homology | Function and homology information ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / positive regulation of DNA-binding transcription factor activity / double-strand break repair via nonhomologous end joining / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Lee, J. / Botuyan, M.V. / Thompson, J.R. / Mer, G. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair. Authors: Botuyan, M.V. / Lee, J. / Ward, I.M. / Kim, J.E. / Thompson, J.R. / Chen, J. / Mer, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g3r.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g3r.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g3r_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 2g3r_full_validation.pdf.gz | 447 KB | Display | |
Data in XML | 2g3r_validation.xml.gz | 10 KB | Display | |
Data in CIF | 2g3r_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/2g3r ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g3r | HTTPS FTP |
-Related structure data
Related structure data | 2fhdC 2ig0C 1xniS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13944.780 Da / Num. of mol.: 1 Fragment: Tandem tutor domains, residues 1484-1603 (SWS-Q12888) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12888 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2% PEG 400, 0.1MHEPES/Na, 2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→26.8 Å / Num. obs: 32860 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1XNI Resolution: 1.25→26.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.756 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.065 / 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: 19.886 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→26.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.278 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 6.591 Å / Origin y: 0.719 Å / Origin z: 11.629 Å
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