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- PDB-3k75: X-ray crystal structure of reduced XRCC1 bound to DNA pol beta ca... -

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Basic information

Entry
Database: PDB / ID: 3k75
TitleX-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain
Components
  • DNA polymerase beta
  • DNA repair protein XRCC1
KeywordsDNA BINDING PROTEIN / allosteric disulfide / XRCC1 / pol beta / DNA damage / DNA repair / Nucleus / Phosphoprotein / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Magnesium / Metal-binding / Methylation / Nucleotidyltransferase / Transferase / DNA-BINDING PROTEIN
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 / 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 / poly-ADP-D-ribose binding / Ub-specific processing proteases / 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 / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) lyase / Gap-filling DNA repair synthesis and ligation in GG-NER / response to organic substance / 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 / in utero embryonic development / microtubule / DNA replication / chromosome, telomeric region / damaged DNA binding / DNA-directed DNA polymerase / response to hypoxia / DNA-directed DNA polymerase activity / lyase activity / response to xenobiotic stimulus / inflammatory response / 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, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / Galactose-binding domain-like / DNA polymerase beta, palm domain ...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 / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / Galactose-binding domain-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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / Galactose-binding-like domain superfamily / DNA polymerase; domain 1 / Jelly Rolls / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase beta / DNA repair protein XRCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.95 Å
AuthorsCuneo, M.J. / 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
DepositionOct 12, 2009Deposition 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 5, 2012Group: Derived calculations
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_keywords / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA repair protein XRCC1
C: DNA repair protein XRCC1
D: DNA polymerase beta
E: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)100,7934
Polymers100,7934
Non-polymers00
Water0
1
B: DNA repair protein XRCC1
D: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)50,3972
Polymers50,3972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: DNA repair protein XRCC1
E: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)50,3972
Polymers50,3972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.770, 44.050, 152.770
Angle α, β, γ (deg.)90.000, 107.210, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12D
22E

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUSERSERBA6 - 1406 - 140
21LEULEUSERSERCB6 - 1406 - 140
12SERSERPROPRODC95 - 3306 - 241
22SERSERPROPROED95 - 3306 - 241

NCS ensembles :
ID
1
2

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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.: 2 / Fragment: N-terminal domain (UNP residues 1 to 183)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: XRCC1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18887
#2: Protein DNA polymerase beta /


Mass: 29336.111 Da / Num. of mol.: 2 / Fragment: UNP residues 91 to 335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Rattus / Gene: Polb / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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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: 2.24 Å3/Da / Density % sol: 45.18 %
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 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Sep 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. obs: 19123 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.334 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.7
Reflection shellResolution: 2.95→3.03 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 4872 / Num. unique all: 1376 / Num. unique obs: 1376 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2.95→24.47 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.813 / Occupancy max: 1 / Occupancy min: 0 / SU B: 49.195 / SU ML: 0.417 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.295 957 5 %RANDOM
Rwork0.242 ---
all0.245 ---
obs0.245 19123 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 137.8 Å2 / Biso mean: 51.723 Å2 / Biso min: 14.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20.35 Å2
2--0.48 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.95→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 0 0 6282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226481
X-RAY DIFFRACTIONr_bond_other_d00.025836
X-RAY DIFFRACTIONr_angle_refined_deg0.8421.968747
X-RAY DIFFRACTIONr_angle_other_deg0.789313618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41423.576316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.602151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7171559
X-RAY DIFFRACTIONr_chiral_restr0.0720.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217239
X-RAY DIFFRACTIONr_gen_planes_other00.021334
X-RAY DIFFRACTIONr_mcbond_it2.5441.53986
X-RAY DIFFRACTIONr_mcbond_other1.3251.51617
X-RAY DIFFRACTIONr_mcangle_it4.68226454
X-RAY DIFFRACTIONr_scbond_it3.25132495
X-RAY DIFFRACTIONr_scangle_it4.5144.52293
X-RAY DIFFRACTIONr_rigid_bond_restr4.119312317
X-RAY DIFFRACTIONr_sphericity_bonded11.941312185
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1904MEDIUM POSITIONAL0.70.5
1B1904MEDIUM THERMAL6.792
2D3696MEDIUM POSITIONAL0.320.5
2D3696MEDIUM THERMAL3.962
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 68 -
Rwork0.355 1287 -
all-1355 -
obs-1326 100 %

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