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- PDB-1imo: NMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1imo
TitleNMR STRUCTURE OF HUMAN DNA LIGASE IIIALPHA BRCT DOMAIN
ComponentsDNA LIGASE III
KeywordsLIGASE / parallel beta sheet
Function / homology
Function and homology information


DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Strand-asynchronous mitochondrial DNA replication / double-strand break repair via alternative nonhomologous end joining / lagging strand elongation / HDR through MMEJ (alt-NHEJ) / Resolution of AP sites via the single-nucleotide replacement pathway ...DNA ligase III-XRCC1 complex / negative regulation of mitochondrial DNA replication / DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / Strand-asynchronous mitochondrial DNA replication / double-strand break repair via alternative nonhomologous end joining / lagging strand elongation / HDR through MMEJ (alt-NHEJ) / Resolution of AP sites via the single-nucleotide replacement pathway / DNA biosynthetic process / mitochondrial DNA repair / 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 / base-excision repair / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / mitochondrial matrix / cell division / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase 3, BRCT domain / DNA ligase 3 BRCT 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal ...DNA ligase 3, BRCT domain / DNA ligase 3 BRCT 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 AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / BRCT domain / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
Model type detailsminimized average
AuthorsKrishnan, V.V. / Thornton, K.H. / Thelen, M.P. / Cosman, M.
Citation
Journal: Biochemistry / Year: 2001
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: Journal: Protein Expr.Purif. / Year: 2001
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
DepositionMay 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA LIGASE III


Theoretical massNumber of molelcules
Total (without water)9,9851
Polymers9,9851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 299structure with the least restraint violations,structure with the lowest energy, target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein DNA LIGASE III / E.C.6.5.1.1 / POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP]


Mass: 9985.422 Da / Num. of mol.: 1 / Fragment: BRCT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P49916, DNA ligase (ATP)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
141HNHA
151DQF-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 50 mM NaH2PO4, 150 mM NaCl, 25 mM d10-DTTT / Solvent system: 90-95% H2O and 10-5% D2O
Sample conditionsIonic strength: 0.4-1.0 mM / pH: 6.6 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2.3MSI Inc.processing
Felix2.3MSI Inc.data analysis
DYANA1.5Wuthrich et al.structure solution
DYANA1.5Wuthrich et al.refinement
RefinementMethod: 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 representativeSelection criteria: minimized average structure
NMR ensembleConformer 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

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