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- PDB-3jve: Crystal Structure of the Sixth BRCT Domain of TopBP1 -

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Basic information

Entry
Database: PDB / ID: 3jve
TitleCrystal Structure of the Sixth BRCT Domain of TopBP1
ComponentsDNA topoisomerase 2-binding protein 1
KeywordsPROTEIN BINDING / BRCT domain / DNA damage / DNA repair / DNA-binding / Nucleus / Phosphoprotein / Polymorphism / Ubl conjugation / DNA BINDING PROTEIN
Function / homology
Function and homology information


broken chromosome clustering / BRCA1-B complex / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / protein localization to site of double-strand break / DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining ...broken chromosome clustering / BRCA1-B complex / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / protein localization to site of double-strand break / DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / chromosome organization / DNA replication initiation / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / condensed nuclear chromosome / male germ cell nucleus / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / spindle pole / actin cytoskeleton / site of double-strand break / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / nuclear body / DNA repair / centrosome / DNA damage response / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.34 Å
AuthorsLeung, C.C. / Kellogg, E. / Baker, D. / Glover, J.N.M.
CitationJournal: Protein Sci. / Year: 2010
Title: Insights from the crystal structure of the sixth BRCT domain of topoisomerase IIbeta binding protein 1.
Authors: Leung, C.C. / Kellogg, E. / Kuhnert, A. / Hanel, F. / Baker, D. / Glover, J.N.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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

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Assembly

Deposited unit
A: DNA topoisomerase 2-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,4131
Polymers12,4131
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.767, 51.824, 62.086
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 topoisomerase 2-binding protein 1 / DNA topoisomerase II-binding protein 1 / DNA topoisomerase IIbeta-binding protein 1 / TopBP1


Mass: 12412.957 Da / Num. of mol.: 1 / Fragment: C-terminus (BRCT) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOPBP1, KIAA0259 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92547
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Tris-HCl pH 6.8, PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 26433 / % possible obs: 99 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.054 / Χ2: 0.764 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.34-1.393.30.35723960.48191.6
1.39-1.445.30.30826110.48899.4
1.44-1.516.70.24826110.533100
1.51-1.597.10.18326300.593100
1.59-1.697.20.14126440.64100
1.69-1.827.20.10826440.747100
1.82-27.20.08826711.082100
2-2.297.20.07526650.959100
2.29-2.8970.04327270.815100
2.89-506.90.03128340.98899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.85 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å16.31 Å
Translation2.5 Å16.31 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→39.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.173 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.919 / SU B: 1.222 / SU ML: 0.024 / SU R Cruickshank DPI: 0.053 / SU Rfree: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.173 1336 5.1 %RANDOM
Rwork0.158 ---
obs0.159 26385 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.13 Å2 / Biso mean: 12.118 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.36 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.34→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 0 153 971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021851
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9461167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8875110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1442440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85715155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.876154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021656
X-RAY DIFFRACTIONr_mcbond_it0.9941.5505
X-RAY DIFFRACTIONr_mcangle_it1.6042832
X-RAY DIFFRACTIONr_scbond_it2.223346
X-RAY DIFFRACTIONr_scangle_it3.3124.5327
X-RAY DIFFRACTIONr_rigid_bond_restr1.2573851
X-RAY DIFFRACTIONr_sphericity_free4.0423153
X-RAY DIFFRACTIONr_sphericity_bonded2.8243818
LS refinement shellResolution: 1.339→1.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 75 -
Rwork0.255 1644 -
all-1719 -
obs--88.61 %
Refinement TLS params.Method: refined / Origin x: 9.378 Å / Origin y: 72.477 Å / Origin z: 10.097 Å
111213212223313233
T0.013 Å20.0036 Å2-0.0009 Å2-0.0287 Å2-0.0124 Å2--0.014 Å2
L1.1715 °2-0.2742 °2-0.0716 °2-0.6469 °20.2469 °2--0.5397 °2
S-0.035 Å °-0.1002 Å °0.0457 Å °0.028 Å °0.0203 Å °-0.0039 Å °0.0002 Å °-0.012 Å °0.0148 Å °

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