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Open data
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Basic information
Entry | Database: PDB / ID: 1imo | ||||||
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Title | NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN | ||||||
![]() | DNA LIGASE III | ||||||
![]() | LIGASE / parallel beta sheet | ||||||
Function / homology | ![]() DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / mitochondrial DNA repair ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / base-excision repair, DNA ligation / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA ligation / HDR through MMEJ (alt-NHEJ) / lagging strand elongation / mitochondrial DNA repair / Resolution of AP sites via the single-nucleotide replacement pathway / DNA biosynthetic process / double-strand break repair via alternative nonhomologous end joining / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / mitochondrion organization / double-strand break repair via homologous recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / cell division / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics | ||||||
Model type details | minimized average | ||||||
![]() | Krishnan, V.V. / Thornton, K.H. / Thelen, M.P. / Cosman, M. | ||||||
![]() | ![]() Title: Solution structure and backbone dynamics of the human DNA ligase IIIalpha BRCT domain Authors: Krishnan, V.V. / Thornton, K.H. / Thelen, M.P. / Cosman, M. #1: ![]() Title: Expression, purification, and biophysical characterization of the BRCT domain of human DNA ligase III alpha Authors: Cosman, M. / Krishnan, V.V. / Thornton, K.H. / Thelen, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.8 KB | Display | ![]() |
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PDB format | ![]() | 30.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9985.422 Da / Num. of mol.: 1 / Fragment: BRCT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy |
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Sample preparation
Details | Contents: 50 mM NaH2PO4, 150 mM NaCl, 25 mM d10-DTTT / Solvent system: 90-95% H2O and 10-5% D2O |
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Sample conditions | Ionic strength: 0.4-1.0 mM / pH: 6.6 / Pressure: ambient / Temperature: 288 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, torsion angle dynamics Software ordinal: 1 Details: the structures are based on a total of 1072 restraints, 979 NOE-derived distance constraints, 25 dihedral angle restraints, 54 H bond restraints from hydrogen bonds | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structure with the least restraint violations,structure with the lowest energy, target function Conformers calculated total number: 299 / Conformers submitted total number: 1 |