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- PDB-1cdz: BRCT DOMAIN FROM DNA-REPAIR PROTEIN XRCC1 -

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Basic information

Entry
Database: PDB / ID: 1cdz
TitleBRCT DOMAIN FROM DNA-REPAIR PROTEIN XRCC1
ComponentsPROTEIN (DNA-REPAIR PROTEIN XRCC1)
KeywordsDNA BINDING PROTEIN / BRCT / BRCA1 / XRCC1 / PROTEIN-PROTEIN INTERACTION
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 / 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 / replication-born double-strand break repair via sister chromatid exchange / cerebellum morphogenesis / single strand break repair / 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 / response to organic substance / 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
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 3.2 Å
AuthorsZhang, X. / Morera, S. / Bates, P. / Whitehead, P. / Coffer, A. / Hainbucher, K. / Nash, R. / Sternberg, M. / Lindahl, T. / Freemont, P.
CitationJournal: EMBO J. / Year: 1998
Title: Structure of an XRCC1 BRCT domain: a new protein-protein interaction module.
Authors: Zhang, X. / Morera, S. / Bates, P.A. / Whitehead, P.C. / Coffer, A.I. / Hainbucher, K. / Nash, R.A. / Sternberg, M.J. / Lindahl, T. / Freemont, P.S.
History
DepositionMar 4, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (DNA-REPAIR PROTEIN XRCC1)


Theoretical massNumber of molelcules
Total (without water)11,4201
Polymers11,4201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.800, 100.800, 72.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98936, 0.00713, 0.14528), (0.0064, -0.9957, 0.09242), (0.14531, 0.09236, 0.98506)
Vector: 95.55961, 1.93427, -6.76424)

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Components

#1: Protein PROTEIN (DNA-REPAIR PROTEIN XRCC1)


Mass: 11419.856 Da / Num. of mol.: 1 / Fragment: C-TERMINAL BRCT DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P18887

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.66 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM FORMATE11
2SODIUM FORMATE12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.5 mg/mlprotein1drop
24 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 7526 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 69 Å2 / Rsym value: 7.2 / Net I/σ(I): 6.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rsym value: 28.6 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
SHARPphasing
CCP4model building
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: SIR / Resolution: 3.2→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHTOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 721 10.3 %RANDOM
Rwork0.224 ---
obs-6921 99 %-
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 0 0 808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT
LS refinement shellResolution: 3.2→3.34 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.386 77 9.8 %
Rwork0.328 754 -
obs--95 %

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