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Yorodumi- PDB-3lgf: Crystal structure of the 53BP1 tandem tudor domain in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lgf | ||||||
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Title | Crystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2 | ||||||
Components |
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Keywords | CELL CYCLE / tandem tudor domains / dimethylated p53 peptide / dna repair / DNA damage / DNA-binding / Methylation / Transcription / Transcription regulation | ||||||
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: 1.5 Å | ||||||
Authors | Roy, S. / Kutateladze, T.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structural insight into p53 recognition by the 53BP1 tandem Tudor domain. Authors: Roy, S. / Musselman, C.A. / Kachirskaia, I. / Hayashi, R. / Glass, K.C. / Nix, J.C. / Gozani, O. / Appella, E. / Kutateladze, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lgf.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lgf.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 3lgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lgf_validation.pdf.gz | 465.6 KB | Display | wwPDB validaton report |
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Full document | 3lgf_full_validation.pdf.gz | 468 KB | Display | |
Data in XML | 3lgf_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 3lgf_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/3lgf ftp://data.pdbj.org/pub/pdb/validation_reports/lg/3lgf | HTTPS FTP |
-Related structure data
Related structure data | 3lglC 3lh0C 2g3rS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14029.840 Da / Num. of mol.: 1 / Fragment: Tandem tudor domains (RESIUDES 1484-1603) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12888 | ||||
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#2: Protein/peptide | Mass: 1130.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.24 Å3/Da / Density % sol: 45.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 10, 2009 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.05 Å / Num. all: 75227 / Num. obs: 21342 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Redundancy: 3.52 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2136 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G3R Resolution: 1.5→39.05 Å / SU ML: 0.51 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.114 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati sigma a obs: 0.208 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→39.05 Å
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Refine LS restraints |
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LS refinement shell |
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