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- PDB-1xnt: NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xnt | ||||||
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Title | NMR SOLUTION STRUCTURE OF THE SINGLE-STRAND BREAK REPAIR PROTEIN XRCC1-N-TERMINAL DOMAIN | ||||||
![]() | PROTEIN (DNA-REPAIR PROTEIN XRCC1) | ||||||
![]() | DNA BINDING PROTEIN / XRCC1 / 3D NMR / DNA REPAIR / SINGLE-STRAND BREAK DNA BINDING / DNA POLYMERASE- BETA BINDING / BETA SANDWICH | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | Marintchev, A. / Mullen, G.P. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 867.1 KB | Display | ![]() |
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-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: 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.) ![]() ![]() ![]() |
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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- AND DOUBLE-RESONANCE NMR SPECTROSCOPY ON 13C-, 15N-LABELED XRCC1-N-TERMINAL DOMAIN |
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Sample preparation
Details | Contents: H2O AND D2O |
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Sample conditions | Ionic strength: 0.4 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
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: 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 ensemble | 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 ...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 |