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- PDB-1uw0: Solution structure of the zinc-finger domain from DNA ligase IIIa -

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Basic information

Entry
Database: PDB / ID: 1uw0
TitleSolution structure of the zinc-finger domain from DNA ligase IIIa
ComponentsDNA LIGASE III
KeywordsLIGASE / DNA REPAIR / ZINC FINGER / PARP-LIKE FINGER / CELL DIVISION / DNA REPLICATION / NUCLEAR PROTEIN
Function / homology
Function and homology information


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 / mitochondrion organization / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / double-strand break repair via homologous recombination / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / cell cycle / 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 / Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / 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 3, BRCT domain / DNA ligase 3 BRCT domain / Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / 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. / 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 / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Zinc finger, PARP-type / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKulczyk, A.W. / Yang, J.-C. / Neuhaus, D.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution Structure and DNA Binding of the Zinc-Finger Domain from DNA Ligase Iiialpha
Authors: Kulczyk, A.W. / Yang, J.-C. / Neuhaus, D.
History
DepositionJan 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA LIGASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3122
Polymers13,2461
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 50LOW RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein DNA LIGASE III / POLYDEOXYRIBONUCLEOTIDE SYNTHASE [ATP]


Mass: 13246.342 Da / Num. of mol.: 1 / Fragment: ZINC-FINGER DOMAIN, RESIDUES 1-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RP / References: UniProt: P49916, DNA ligase (ATP)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Compound detailsINTERACTS WITH DNA-REPAIR PROTEIN XRCC1 AND CAN CORRECT DEFECTIVE DNA STRAND-BREAK REPAIR AND ...INTERACTS WITH DNA-REPAIR PROTEIN XRCC1 AND CAN CORRECT DEFECTIVE DNA STRAND-BREAK REPAIR AND SISTER CHROMATID EXCHANGE FOLLOWING TREATMENT WITH IONIZING RADIATION AND ALKYLATING AGENTS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HSQC
151CBCANH
161CBCA(CO)NH
171HBHANH
181HBHA(CO)NH
191(H)CCH-TOCSY
1101(H)CCH-COSY
111115N NOESY-HSQC
112115N HSQC-NOESY-HSQC
113113C NOESY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED DNA-LIGASE III ZINC FINGER DOMAIN.

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Sample preparation

Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
XwinNMRstructure solution
Sparkystructure solution
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOW RESTRAINT VIOLATIONS / Conformers calculated total number: 50 / Conformers submitted total number: 28

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