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- PDB-3w1g: Crystal Structure of Human DNA ligase IV-Artemis Complex (Native) -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w1g | ||||||
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Title | Crystal Structure of Human DNA ligase IV-Artemis Complex (Native) | ||||||
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![]() | LIGASE / DNA ligase / non homologous end joining / DNA repair / XRCC4 | ||||||
Function / homology | ![]() DNA ligation involved in DNA recombination / positive regulation of chromosome organization / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity ...DNA ligation involved in DNA recombination / positive regulation of chromosome organization / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / single-stranded DNA endodeoxyribonuclease activity / immunoglobulin V(D)J recombination / nonhomologous end joining complex / 5'-3' exonuclease activity / DNA ligation / V(D)J recombination / double-strand break repair via classical nonhomologous end joining / isotype switching / 5'-3' DNA exonuclease activity / positive regulation of neurogenesis / nucleotide-excision repair, DNA gap filling / response to ionizing radiation / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / ligase activity / somatic stem cell population maintenance / response to X-ray / chromosome organization / interstrand cross-link repair / condensed chromosome / telomere maintenance / B cell differentiation / neurogenesis / stem cell proliferation / central nervous system development / cellular response to ionizing radiation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / positive regulation of fibroblast proliferation / double-strand break repair / fibroblast proliferation / T cell differentiation in thymus / endonuclease activity / neuron apoptotic process / adaptive immune response / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / cell cycle / cell division / intracellular membrane-bounded organelle / Golgi apparatus / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ochi, T. / Blundell, T.L. | ||||||
![]() | ![]() Title: Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair Authors: Ochi, T. / Gu, X. / Blundell, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.3 KB | Display | ![]() |
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PDB format | ![]() | 208.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 806 KB | Display | ![]() |
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Full document | ![]() | 811.1 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3w1bSC ![]() 3w5oC 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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Unit cell |
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Components
#1: Protein | Mass: 69538.312 Da / Num. of mol.: 1 / Fragment: Catalytic region, UNP residues 1-609 Source method: isolated from a genetically manipulated source Details: Hippocampus / Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 1452.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→68.26 Å / Num. all: 28941 / Num. obs: 27784 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 46.91 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3W1B Resolution: 2.55→59.462 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.26 Å2 / Biso mean: 59.456 Å2 / Biso min: 22.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→59.462 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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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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