+Open data
-Basic information
Entry | Database: PDB / ID: 5gox | ||||||
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Title | Eukaryotic Rad50 Functions as A Rod-shaped Dimer | ||||||
Components | DNA repair protein RAD50 | ||||||
Keywords | HYDROLASE / DNA repair | ||||||
Function / homology | Function and homology information chromosome, telomeric region => GO:0000781 / telomeric 3' overhang formation / : / Mre11 complex / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / regulation of mitotic recombination / chromosome organization involved in meiotic cell cycle / Hydrolases; Acting on acid anhydrides / chromatin => GO:0000785 ...chromosome, telomeric region => GO:0000781 / telomeric 3' overhang formation / : / Mre11 complex / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / regulation of mitotic recombination / chromosome organization involved in meiotic cell cycle / Hydrolases; Acting on acid anhydrides / chromatin => GO:0000785 / G-quadruplex DNA binding / adenylate kinase activity / double-stranded telomeric DNA binding / DNA double-strand break processing / telomere maintenance via recombination / positive regulation of telomere maintenance / single-stranded telomeric DNA binding / HDR through MMEJ (alt-NHEJ) / telomere capping / positive regulation of kinase activity / reciprocal meiotic recombination / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / positive regulation of protein autophosphorylation / viral process / telomere maintenance / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein-macromolecule adaptor activity / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.405 Å | ||||||
Authors | Park, Y.B. / Hohl, M. / Padjasek, M. / Jeong, E. / Jin, K.S. / Krezel, A. / Petrini, J.H.J. / Cho, Y. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Eukaryotic Rad50 functions as a rod-shaped dimer Authors: Park, Y.B. / Hohl, M. / Padjasek, M. / Jeong, E. / Jin, K.S. / Krezel, A. / Petrini, J.H.J. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gox.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gox.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/5gox ftp://data.pdbj.org/pub/pdb/validation_reports/go/5gox | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21876.180 Da / Num. of mol.: 2 / Fragment: UNP residues 585-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAD50 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: Q92878, Hydrolases; Acting on acid anhydrides #2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % / Description: hexagonal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: 28 - 30% PEG 600, 0.1 M bis-tris propane, 3% 1, 6-hexanediol, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9766 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2014 |
Radiation | Monochromator: Si 4-crystal channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9766 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16270 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.98 / Rsym value: 0.07 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 2.4→2.44 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.405→28.221 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.405→28.221 Å
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Refine LS restraints |
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LS refinement shell |
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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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