+Open data
-Basic information
Entry | Database: PDB / ID: 4gb0 | ||||||
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Title | Crystal Structure of the RING domain of RNF168 | ||||||
Components | E3 ubiquitin-protein ligase RNF168 | ||||||
Keywords | LIGASE / RING domain / E3 ligase / E2 | ||||||
Function / homology | Function and homology information histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / isotype switching / double-strand break repair via classical nonhomologous end joining / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / nucleosome binding ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / isotype switching / double-strand break repair via classical nonhomologous end joining / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / nucleosome binding / interstrand cross-link repair / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / positive regulation of DNA repair / ubiquitin binding / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / double-strand break repair via nonhomologous end joining / ubiquitin-protein transferase activity / double-strand break repair / 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 / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / chromatin binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Zhang, X.Q. / Wang, C.L. / Zang, J.Y. | ||||||
Citation | Journal: Cell Cycle / Year: 2013 Title: Structural basis for role of ring finger protein RNF168 RING domain Authors: Zhang, X.Q. / Chen, J. / Wu, M. / Wu, H. / Arokiaraj, A.W. / Wang, C.L. / Zhang, W. / Tao, Y. / Huen, M.S. / Zang, J.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gb0.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gb0.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 4gb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/4gb0 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/4gb0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13922.087 Da / Num. of mol.: 1 / Fragment: UNP residues 1-111 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF168 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) References: UniProt: Q8IYW5, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||
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#2: Chemical | ChemComp-MLI / | ||
#3: Chemical | #4: 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: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.6M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 4894 / Num. obs: 4871 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.6→2.74 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→35.47 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.307 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.794 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→35.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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