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- PDB-3lqc: X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta P... -
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Basic information
Entry | Database: PDB / ID: 3lqc | ||||||
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Title | X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain | ||||||
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![]() | DNA BINDING PROTEIN / ALLOSTERIC DISULFIDE / SCAFFOLDING PROTEIN / DNA REPAIR / DNA DAMAGE / Nucleus / Phosphoprotein / Polymorphism / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Magnesium / Metal-binding / Nucleotidyltransferase / Sodium / Transferase / DNA-BINDING PROTEIN | ||||||
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 / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision 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 / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / ADP-D-ribose modification-dependent protein binding / somatic diversification of immunoglobulins / negative regulation of protein ADP-ribosylation / Ub-specific processing proteases / 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 / immunoglobulin heavy chain V-D-J recombination / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / : / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / Gap-filling DNA repair synthesis and ligation in GG-NER / spindle microtubule / hippocampus development / response to gamma radiation / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / DNA replication / in utero embryonic development / microtubule / damaged DNA binding / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / response to hypoxia / lyase activity / response to xenobiotic stimulus / inflammatory response / DNA damage response / chromatin / nucleolus / apoptotic process / enzyme binding / protein-containing complex / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cuneo, M.J. / Krahn, J.M. / London, R.E. | ||||||
![]() | ![]() Title: Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity. Authors: Cuneo, M.J. / London, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.6 KB | Display | ![]() |
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PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3k75C ![]() 3k77C ![]() 1xnaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21060.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 23523.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-CO3 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20-25% PEG 3350, 0.2-0.3M TRI-POTASSIUM CITRATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 1, 2008 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→30 Å / Num. all: 17765 / Num. obs: 17765 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 29.723 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 19.02 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 9000 / Num. unique obs: 1270 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1XNA Resolution: 2.349→24.628 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.15 / σ(F): 1.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.938 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.69 Å2 / Biso mean: 25.071 Å2 / Biso min: 9.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.349→24.628 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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