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- PDB-3uen: Crystal structure of TopBP1 BRCT4/5 domains -

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Basic information

Entry
Database: PDB / ID: 3uen
TitleCrystal structure of TopBP1 BRCT4/5 domains
ComponentsDNA topoisomerase 2-binding protein 1
KeywordsPEPTIDE BINDING PROTEIN / BRCT domain / phospho-peptide binding
Function / homology
Function and homology information


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 alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / HDR through Single Strand Annealing (SSA) ...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 alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / response to ionizing radiation / site of DNA damage / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication initiation / chromosome organization / 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
THIOCYANATE ION / DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLeung, C.C. / Glover, J.N.M.
CitationJournal: Structure / Year: 2013
Title: Structural insights into recognition of MDC1 by TopBP1 in DNA replication checkpoint control.
Authors: Leung, C.C. / Sun, L. / Gong, Z. / Burkat, M. / Edwards, R. / Assmus, M. / Chen, J. / Glover, J.N.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7577
Polymers22,2381
Non-polymers5196
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.902, 48.801, 126.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-1093-

HOH

21A-1133-

HOH

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Components

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


Mass: 22238.371 Da / Num. of mol.: 1 / Fragment: BRCT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0259, TOPBP1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q92547
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, NaSCN, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 18140 / Num. obs: 18140 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.933.70.497199.2
1.93-1.973.90.4431100
1.97-2.013.90.3841100
2.01-2.0540.2851100
2.05-2.093.80.258199.8
2.09-2.143.90.2271100
2.14-2.1940.2051100
2.19-2.253.80.192199.9
2.25-2.323.90.175199.9
2.32-2.393.90.1441100
2.39-2.483.90.1351100
2.48-2.583.90.121199.9
2.58-2.73.90.109199.7
2.7-2.843.90.0921100
2.84-3.023.80.077199.9
3.02-3.253.80.0651100
3.25-3.583.80.05199.7
3.58-4.093.60.034199.6
4.09-5.163.90.03199.2
5.16-503.60.026198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.63 Å
Translation2.5 Å38.63 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.59 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2237 927 5.11 %
Rwork0.175 --
obs0.1775 18137 99.67 %
all-18137 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.73 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.5852 Å20 Å20 Å2
2--9.5631 Å20 Å2
3---6.0125 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 33 238 1773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111603
X-RAY DIFFRACTIONf_angle_d1.3472174
X-RAY DIFFRACTIONf_dihedral_angle_d14.537597
X-RAY DIFFRACTIONf_chiral_restr0.085252
X-RAY DIFFRACTIONf_plane_restr0.005274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.28071420.23022376X-RAY DIFFRACTION99
2.0002-2.12550.24241330.18142427X-RAY DIFFRACTION100
2.1255-2.28960.23871270.1812395X-RAY DIFFRACTION100
2.2896-2.520.22461310.17542443X-RAY DIFFRACTION100
2.52-2.88450.20971270.17362466X-RAY DIFFRACTION100
2.8845-3.63370.22451270.15472496X-RAY DIFFRACTION100
3.6337-38.59820.20841400.17612607X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.4566 Å / Origin y: 49.5704 Å / Origin z: 76.5804 Å
111213212223313233
T0.0137 Å20.0141 Å20.0119 Å2-0.0113 Å20.0277 Å2--0.0078 Å2
L0.1582 °20.0587 °20.002 °2-0.4039 °2-0.1843 °2--0.3347 °2
S0.0131 Å °0.0302 Å °0.0333 Å °-0.0343 Å °-0.0198 Å °-0.0287 Å °-0.0395 Å °0.0233 Å °0.0076 Å °
Refinement TLS groupSelection details: CHAIN A

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