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- PDB-3olc: Crystal structure of the N-terminal region of TopBP1 -

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Basic information

Entry
Database: PDB / ID: 3olc
TitleCrystal structure of the N-terminal region of TopBP1
ComponentsDNA topoisomerase 2-binding protein 1
KeywordsDNA BINDING PROTEIN / BRCT domain / DNA repair / Rad9
Function / homology
Function and homology information


broken chromosome clustering / BRCA1-B complex / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / mitotic DNA replication checkpoint signaling / HDR through Single Strand Annealing (SSA) ...broken chromosome clustering / BRCA1-B complex / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / mitotic DNA replication checkpoint signaling / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / response to ionizing radiation / double-strand break repair via alternative nonhomologous end joining / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication initiation / chromosome organization / protein serine/threonine kinase activator activity / condensed nuclear chromosome / DNA damage checkpoint signaling / male germ cell nucleus / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / spindle pole / actin cytoskeleton / chromosome / site of double-strand break / 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 / SAD / Resolution: 2.4 Å
AuthorsHuo, Y.G. / Bai, L. / Xu, M. / Jiang, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structure of the N-terminal region of human Topoisomerase II beta binding protein 1
Authors: Huo, Y.G. / Bai, L. / Xu, M. / Jiang, T.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: DNA topoisomerase 2-binding protein 1


Theoretical massNumber of molelcules
Total (without water)35,2301
Polymers35,2301
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.730, 115.730, 115.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein DNA topoisomerase 2-binding protein 1 / DNA topoisomerase II-binding protein 1 / DNA topoisomerase II-beta-binding protein 1 / TopBP1


Mass: 35230.430 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOPBP1, KIAA0259 / Plasmid: Pet24a / Production host: Escherichia coli (E. coli) / References: UniProt: Q92547
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M MES, 11%(w/v) PEG3350, 0.85M sodium nitrate, 2mM EDTA, 4mM DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.4→81.833 Å / Num. all: 20506 / Num. obs: 20506 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 4.95 / Num. unique all: 3884 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→81.833 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.631 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.26 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.25787 1048 5.1 %
Rwork0.2208 --
obs0.22267 19410 99.77 %
all-20506 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.904 Å2
Refinement stepCycle: LAST / Resolution: 2.4→81.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 0 59 2334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9573128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30924.571105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7841510
X-RAY DIFFRACTIONr_chiral_restr0.1470.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211710
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3061.51394
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44122270
X-RAY DIFFRACTIONr_scbond_it3.7663931
X-RAY DIFFRACTIONr_scangle_it5.9284.5858
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 83 -
Rwork0.307 1443 -
obs--99.8 %

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