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- PDB-3pc6: X-ray crystal structure of the second XRCC1 BRCT domain. -

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Basic information

Entry
Database: PDB / ID: 3pc6
TitleX-ray crystal structure of the second XRCC1 BRCT domain.
ComponentsDNA repair protein XRCC1
KeywordsDNA BINDING PROTEIN / DNA repair / BRCT domain / Protein:protein interactions / DNA ligase III-alpha BRCT2 domain
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / HDR through MMEJ (alt-NHEJ) / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / ADP-D-ribose modification-dependent protein binding / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of protein ADP-ribosylation ...Resolution of AP sites via the single-nucleotide replacement pathway / HDR through MMEJ (alt-NHEJ) / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / ADP-D-ribose modification-dependent protein binding / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / response to hydroperoxide / site of DNA damage / : / hippocampus development / base-excision repair / double-strand break repair via nonhomologous end joining / chromosome, telomeric region / response to hypoxia / response to xenobiotic stimulus / DNA repair / 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 / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / 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 / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA repair protein XRCC1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCuneo, M.J. / Krahn, J.M. / London, R.E.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: The structural basis for partitioning of the XRCC1/DNA ligase III-{alpha} BRCT-mediated dimer complexes.
Authors: Cuneo, M.J. / Gabel, S.A. / Krahn, J.M. / Ricker, M.A. / London, R.E.
History
DepositionOct 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein XRCC1
B: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)25,1762
Polymers25,1762
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area12040 Å2
Unit cell
Length a, b, c (Å)44.230, 56.850, 100.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12588.151 Da / Num. of mol.: 2 / Fragment: XRCC1 second BRCT domain (unp residues 534-630)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xrcc-1, Xrcc1 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-RIL / References: UniProt: Q60596
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6M NaFormate, 0.2M NaHEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2010
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 20146 / Num. obs: 20146 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.062 / Χ2: 1.1 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.973.50.23116681.178182.8
1.97-2.054.10.21718961.111193.8
2.05-2.144.90.19619971.151198.2
2.14-2.255.30.16220331.163199.6
2.25-2.395.60.13720381.069199.9
2.39-2.585.60.10420631.0861100
2.58-2.845.60.08420421.0081100
2.84-3.255.50.06120781.0411100
3.25-4.095.40.04321041.137199.9
4.09-505.10.03422271.121199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CDZ

1cdz


Resolution: 1.9→37.625 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8469 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1033 5.14 %random
Rwork0.18 ---
obs0.1823 20081 97.35 %-
all-20081 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.968 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 87.94 Å2 / Biso mean: 27.3142 Å2 / Biso min: 9.36 Å2
Baniso -1Baniso -2Baniso -3
1-8.5994 Å2-0 Å2-0 Å2
2---0.3794 Å2-0 Å2
3----8.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 0 182 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061831
X-RAY DIFFRACTIONf_angle_d0.8632498
X-RAY DIFFRACTIONf_chiral_restr0.068242
X-RAY DIFFRACTIONf_plane_restr0.004337
X-RAY DIFFRACTIONf_dihedral_angle_d16.095662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.99930.29171350.2062328246385
1.9993-2.12460.21471450.18962655280097
2.1246-2.28860.25221380.17742754289299
2.2886-2.51890.26271570.189327492906100
2.5189-2.88330.22261670.193627712938100
2.8833-3.63210.20131520.163428282980100
3.6321-37.63250.20531390.171129633102100

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