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Yorodumi- PDB-6bkg: Human LigIV catalytic domain with bound DNA-adenylate intermediat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bkg | |||||||||||||||
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Title | Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation | |||||||||||||||
Components |
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Keywords | LIGASE/DNA / DNA double-strand break repair / ligase / nonhomologous end-joining / LIGASE-DNA complex | |||||||||||||||
Function / homology | Function and homology information 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 / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / V(D)J recombination / isotype switching / double-strand break repair via classical nonhomologous end joining / nucleotide-excision repair, DNA gap filling / positive regulation of neurogenesis / condensed chromosome / 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 / neurogenesis / stem cell proliferation / Nonhomologous End-Joining (NHEJ) / central nervous system development / cellular response to ionizing radiation / response to gamma radiation / positive regulation of fibroblast proliferation / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / double-strand break repair / chromosome, telomeric region / fibroblast proliferation / T cell differentiation in thymus / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / cell division / intracellular membrane-bounded organelle / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | |||||||||||||||
Authors | Moon, A.F. / Tumbale, P.P. / Schellenberg, M.J. / Williams, R.S. / Williams, J.G. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, B. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis. Authors: Kaminski, A.M. / Tumbale, P.P. / Schellenberg, M.J. / Williams, R.S. / Williams, J.G. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bkg.cif.gz | 294.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bkg.ent.gz | 229.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bkg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6bkg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6bkg_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 6bkg_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bkg ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bkg | HTTPS FTP |
-Related structure data
Related structure data | 6bkfC 3w5oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 70695.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pOPINS / Details (production host): N-terminal SUMO fusion tag / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) pLysS / References: UniProt: P49917, DNA ligase (ATP) |
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-DNA chain , 3 types, 3 molecules PTD
#2: DNA chain | Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 5486.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2138.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 117 molecules
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-EDO / | #8: Chemical | ChemComp-AMP / | #9: 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: 2.51 Å3/Da / Density % sol: 50.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 78.2mM HEPES pH 7.5, 15.64% PEG4000, 7.82% isopropanol, 13.8% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 22, 2016 / Details: ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 32742 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.798 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Rsym value: 0.065 / Χ2: 0.928 / Net I/σ(I): 31.16 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.45 / Num. unique obs: 1598 / CC1/2: 0.798 / Rpim(I) all: 0.334 / Rrim(I) all: 0.911 / Rsym value: 0.846 / Χ2: 0.898 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W5O Resolution: 2.402→39.2 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 25.7 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→39.2 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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