- PDB-7d9k: DNA binding domain of human DNA Ligase IV - Wild type -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7d9k
Title
DNA binding domain of human DNA Ligase IV - Wild type
Components
DNA ligase 4
Keywords
LIGASE / DBD / Native / ATP dependant ligase.
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 / 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 / condensed chromosome / 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 / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / chromosome, telomeric region / cell division / intracellular membrane-bounded organelle / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function
DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. ...DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
DNAligase4 / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4
Mass: 27627.938 Da / Num. of mol.: 1 / Fragment: DNA binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pET15b, pENH240 Details (production host): DBDLigIV cloned at NdeI and BamHI restriction site in pET15b Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon Plus RIPL / References: UniProt: P49917, DNA ligase (ATP)
Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.18 Å3/Da / Density % sol: 61.33 % Description: Cubic crystals of DBD LigIV-Wt exhibiting a characteristic bipyramidal shape. Actual dimensions of the largest crystal are of the order of 0.25 um to 0.26 mm.
Crystal grow
Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 20 % SOKALAN CP 42, 5% Methanol / Temp details: Rubarth Incubator Vibration Free
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Data collection
Diffraction
Mean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
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