+Open data
-Basic information
Entry | Database: PDB / ID: 3i0m | ||||||
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Title | Structure of the S. pombe Nbs1 FHA/BRCT-repeat domain | ||||||
Components | DNA repair and telomere maintenance protein nbs1 | ||||||
Keywords | CELL CYCLE / FHA / BRCT-repeat / DNA-damage / Chromosomal protein / DNA damage / DNA repair / Nucleus / Phosphoprotein / Telomere / GENE REGULATION | ||||||
Function / homology | Function and homology information DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / chromosome, telomeric repeat region / chromatin-protein adaptor activity / DNA double-strand break processing / telomere maintenance via recombination ...DNA Damage/Telomere Stress Induced Senescence / HDR through MMEJ (alt-NHEJ) / Sensing of DNA Double Strand Breaks / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Mre11 complex / chromosome, telomeric repeat region / chromatin-protein adaptor activity / DNA double-strand break processing / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / DNA duplex unwinding / protein localization to chromosome, telomeric region / mitotic G2 DNA damage checkpoint signaling / telomere maintenance / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / damaged DNA binding / molecular adaptor activity / DNA repair / nucleus Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Clapperton, J.A. / Lloyd, J. / Chapman, J.R. / Jackson, S.P. / Smerdon, S.J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: A supramodular FHA/BRCT-repeat architecture mediates Nbs1 adaptor function in response to DNA damage Authors: Lloyd, J. / Chapman, J.R. / Clapperton, J.A. / Haire, L.F. / Hartsuiker, E. / Li, J. / Carr, A.M. / Jackson, S.P. / Smerdon, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i0m.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i0m.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3i0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/3i0m ftp://data.pdbj.org/pub/pdb/validation_reports/i0/3i0m | HTTPS FTP |
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-Related 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: 36925.781 Da / Num. of mol.: 1 Fragment: N-terminal FHA/BRCT-repeat domain, UNP residues 1-324 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: nbs1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43070 |
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#2: Chemical | ChemComp-GOL / |
#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: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 8% PEG6000, 0.1M MES, 0.1M MgCl2, pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9698 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2008 |
Radiation | Monochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9698 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 19822 / Num. obs: 19822 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.45 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.619 / SU ML: 0.271 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.269 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.665 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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