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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
TitleX-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain
Components
  • DNA polymerase beta
  • DNA repair protein XRCC1
KeywordsDNA 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
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / 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 ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / 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 / poly-ADP-D-ribose binding / Ub-specific processing proteases / positive regulation of single strand break repair / cerebellum morphogenesis / voluntary musculoskeletal movement / single strand break repair / 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 / pyrimidine dimer repair / 5'-deoxyribose-5-phosphate lyase activity / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / hippocampus development / Gap-filling DNA repair synthesis and ligation in GG-NER / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / microtubule binding / neuron apoptotic process / in utero embryonic development / microtubule / response to ethanol / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / chromosome, telomeric region / response to hypoxia / DNA replication / lyase activity / inflammatory response / response to xenobiotic stimulus / apoptotic process / DNA damage response / chromatin / nucleolus / enzyme binding / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm ...DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Galactose-binding domain-like / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / DNA polymerase beta / DNA repair protein XRCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.349 Å
AuthorsCuneo, M.J. / Krahn, J.M. / London, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.
Authors: Cuneo, M.J. / London, R.E.
History
DepositionFeb 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_keywords / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein XRCC1
B: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6674
Polymers44,5842
Non-polymers832
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 75.240, 126.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA repair protein XRCC1 / X-ray repair cross-complementing protein 1


Mass: 21060.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiens / Gene: XRCC1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: P18887
#2: Protein DNA polymerase beta


Mass: 23523.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Polb / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 1, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XNA

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
RfactorNum. reflection% reflectionSelection details
Rfree0.25 889 5 %random
Rwork0.189 ---
obs0.192 17764 99.9 %-
all-17765 --
Solvent computationShrinkage 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 parametersBiso max: 82.69 Å2 / Biso mean: 25.071 Å2 / Biso min: 9.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.567 Å20 Å2-0 Å2
2--2.567 Å20 Å2
3----5.133 Å2
Refinement stepCycle: LAST / Resolution: 2.349→24.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 4 234 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062795
X-RAY DIFFRACTIONf_angle_d0.923772
X-RAY DIFFRACTIONf_chiral_restr0.059409
X-RAY DIFFRACTIONf_plane_restr0.004498
X-RAY DIFFRACTIONf_dihedral_angle_d15.8951044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.349-2.4970.3251450.23627512896
2.497-2.6890.2771460.22427722918
2.689-2.9590.2861450.20327622907
2.959-3.3860.2771470.18527922939
3.386-4.2630.2071500.15428362986
4.263-24.6290.2051560.1629623118

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