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- PDB-1xnt: NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1xnt
TitleNMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN
ComponentsPROTEIN (DNA-REPAIR PROTEIN XRCC1)
KeywordsDNA BINDING PROTEIN / XRCC1 / 3D NMR / DNA REPAIR / SINGLE-STRAND BREAK DNA BINDING / DNA POLYMERASE- BETA BINDING / BETA SANDWICH
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / positive regulation of single strand break repair ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / positive regulation of single strand break repair / voluntary musculoskeletal movement / cerebellum morphogenesis / single strand break repair / replication-born double-strand break repair via sister chromatid exchange / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / Gap-filling DNA repair synthesis and ligation in GG-NER / : / hippocampus development / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome, telomeric region / response to hypoxia / response to xenobiotic stimulus / chromatin / nucleolus / enzyme binding / nucleoplasm / nucleus
Similarity search - Function
DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / Galactose-binding domain-like / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / Galactose-binding domain-like / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA repair protein XRCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMarintchev, A. / Mullen, G.P.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Solution structure of the single-strand break repair protein XRCC1 N-terminal domain.
Authors: Marintchev, A. / Mullen, M.A. / Maciejewski, M.W. / Pan, B. / Gryk, M.R. / Mullen, G.P.
History
DepositionFeb 27, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (DNA-REPAIR PROTEIN XRCC1)


Theoretical massNumber of molelcules
Total (without water)20,2461
Polymers20,2461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 6030 OUT OF 60 STRUCTURES IN DYANA, CRITERION: TARGET FUNCTION. X-PLOR REFINEMENT: 23 OUT OF 30 STRUCTURES, CRITERIA: NO NOE RESTRAINT VIOLATIONS > 0.5 A AND NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 5 DEG.
Representative

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Components

#1: Protein PROTEIN (DNA-REPAIR PROTEIN XRCC1) / XRCC1-NTD


Mass: 20245.672 Da / Num. of mol.: 1
Fragment: N-TERMINAL DOMAIN, RESIDUES 1-183. RESIDUES 152-183 ARE DISORDERED AND NOT SHOWN.
Mutation: D179E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUSCell nucleus / Gene: XRCC1 / Plasmid: PET23A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3]PLYSS / References: UniProt: P18887

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
121CBCA(CO)NH
131HNCA
141HN(CO)CA
15115N-EDITED TOCSY
161HCC(CO)NH
171CC(CO)NH
181(H)CCH TOCSY
191HNCO
1101HNHA
1111HNHB
11212D (HB)CB(CGCD)HD
11311H-15N-HSQC
11411H-13C-HSQC
11511H-TOCSY
1161AROMATIC 1H-13C-HSQC
1171HMQC-J
11813D 15N-NOESY
11913D 13C-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE- AND DOUBLE-RESONANCE NMR SPECTROSCOPY ON 13C-, 15N-LABELED XRCC1-N-TERMINAL DOMAIN

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Sample preparation

DetailsContents: H2O AND D2O
Sample conditionsIonic strength: 0.4 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
DYANA1.5structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RMSD (ANGSTROMS) WITH RESPECT TO MEAN: BETA-STRANDS: HEAVY BACKBONE ATOMS 0.26 +/- 0.05; ALL HEAVY ATOMS 0.69 +/- 0.13. RESIDUES 3- ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RMSD (ANGSTROMS) WITH RESPECT TO MEAN: BETA-STRANDS: HEAVY BACKBONE ATOMS 0.26 +/- 0.05; ALL HEAVY ATOMS 0.69 +/- 0.13. RESIDUES 3-76, 83-151 (EXCLUDING THE FLEXIBLE 77-82) : HEAVY BACKBONE ATOMS 0.42 +/- 0.09; ALL HEAVY ATOMS 0.87 +/- 0.12.
NMR ensembleConformer selection criteria: 30 OUT OF 60 STRUCTURES IN DYANA, CRITERION: TARGET FUNCTION. X-PLOR REFINEMENT: 23 OUT OF 30 STRUCTURES, CRITERIA: NO NOE RESTRAINT VIOLATIONS > 0.5 A AND NO DIHEDRAL ...Conformer selection criteria: 30 OUT OF 60 STRUCTURES IN DYANA, CRITERION: TARGET FUNCTION. X-PLOR REFINEMENT: 23 OUT OF 30 STRUCTURES, CRITERIA: NO NOE RESTRAINT VIOLATIONS > 0.5 A AND NO DIHEDRAL ANGLE RESTRAINT VIOLATIONS > 5 DEG.
Conformers calculated total number: 60 / Conformers submitted total number: 23

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