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- PDB-3al2: Crystal Structure of TopBP1 BRCT7/8 -

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Basic information

Entry
Database: PDB / ID: 3al2
TitleCrystal Structure of TopBP1 BRCT7/8
ComponentsDNA topoisomerase 2-binding protein 1
KeywordsDNA BINDING PROTEIN / protein binding / BRCT domain
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
DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLeung, C.C. / Glover, J.N.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular basis of BACH1/FANCJ recognition by TopBP1 in DNA replication checkpoint control
Authors: Leung, C.C. / Gong, Z. / Chen, J. / Glover, J.N.
History
DepositionJul 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,7573
Polymers26,5651
Non-polymers1922
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.583, 32.748, 81.762
Angle α, β, γ (deg.)90.00, 109.32, 90.00
Int Tables number5
Space group name H-MC121

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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: 26565.078 Da / Num. of mol.: 1 / Fragment: BRCT7 and BRCT8, UNP residues 1264-1493
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Li2SO4, Tris-HCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33711 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.068
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.072.70.332192.9
2.07-2.153.10.287198.7
2.15-2.253.40.245199.9
2.25-2.373.60.207199.9
2.37-2.523.80.1581100
2.52-2.713.90.1361100
2.71-2.993.90.0971100
2.99-3.423.90.0641100
3.42-4.313.90.0571100
4.31-5040.032199.8

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
161.1665.83819.154S201
254.1516.40913.791S200.938
349.9416.02414.705S200.16
458.08616.5411.073S200.062
Phasing dmFOM : 0.64 / FOM acentric: 0.64 / FOM centric: 0.73 / Reflection: 16574 / Reflection acentric: 15290 / Reflection centric: 1284
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-19.5840.910.910.89797632165
3.6-5.70.910.920.8523692090279
2.9-3.60.820.820.8529292678251
2.5-2.90.670.670.6628852680205
2.1-2.50.520.510.5849004631269
2-2.10.340.340.3726942579115

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.997 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1671 / SU Rfree: 0.1441 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The SF file contains Friedel pairs under I/F_plus and I/F_minus column.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 902 5.1 %RANDOM
Rwork0.17 ---
obs0.172 17624 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0.12 Å2
2---0.36 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 10 182 1947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221881
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9522566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57723.52388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10615332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211437
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_it0.8771.51137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64321843
X-RAY DIFFRACTIONr_scbond_it2.4983744
X-RAY DIFFRACTIONr_scangle_it4.0644.5710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 69 -
Rwork0.215 1212 -
obs--96.32 %
Refinement TLS params.Method: refined / Origin x: 15.083 Å / Origin y: 28.441 Å / Origin z: 17.813 Å
111213212223313233
T0.0603 Å20.0071 Å2-0.0015 Å2-0.0231 Å20.0013 Å2--0.053 Å2
L0.2562 °2-0.035 °20.2528 °2-0.0956 °2-0.2368 °2--1.9002 °2
S0.0173 Å °0.0784 Å °-0.0051 Å °0.081 Å °0.0116 Å °0.0265 Å °-0.0074 Å °0.0498 Å °-0.0289 Å °

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