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- PDB-7abs: Structure of human DCLRE1C/Artemis in complex with DNA - re-evalu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7abs | ||||||
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Title | Structure of human DCLRE1C/Artemis in complex with DNA - re-evaluation of 6WO0 | ||||||
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![]() | LYASE / Artemis / NHEJ / Nuclease | ||||||
Function / homology | ![]() single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / V(D)J recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) ...single-stranded DNA endodeoxyribonuclease activity / nonhomologous end joining complex / V(D)J recombination / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / response to ionizing radiation / interstrand cross-link repair / telomere maintenance / B cell differentiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / endonuclease activity / adaptive immune response / damaged DNA binding / Hydrolases; Acting on ester bonds / Golgi apparatus / nucleoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Yosaatmadja, Y. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
![]() | ![]() Title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition. Authors: Yosaatmadja, Y. / Baddock, H.T. / Newman, J.A. / Bielinski, M. / Gavard, A.E. / Mukhopadhyay, S.M.M. / Dannerfjord, A.A. / Schofield, C.J. / McHugh, P.J. / Gileadi, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.4 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tt5C ![]() 7af1C ![]() 7afsC ![]() 7afuC ![]() 7agiC ![]() 7apvC ![]() 6wo0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43294.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96SD1, Hydrolases; Acting on ester bonds | ||||
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#2: DNA chain | Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#3: DNA chain | Mass: 3936.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.47 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 50 mM MES pH 6.5, 0.1 M LiCl, 0.01 M MgCl2, 12% PEG 4000 (w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 26, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→35 Å / Num. obs: 32168 / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.97→2.02 Å / Rmerge(I) obs: 0.828 / Num. unique obs: 2189 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WO0 Resolution: 1.97→34.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.358 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.181 / 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: 53.197 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→34.54 Å
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Refine LS restraints |
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