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- PDB-5u6k: Crystal structure of TopBP1 BRCT4/5 in complex with a BLM phospho... -

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Basic information

Entry
Database: PDB / ID: 5u6k
TitleCrystal structure of TopBP1 BRCT4/5 in complex with a BLM phosphopeptide
Components
  • Bloom Sydrome recQ helicase like protein (BLM)
  • DNA topoisomerase 2-binding protein 1
KeywordsPEPTIDE BINDING PROTEIN / BRCT repeat family replication checkpoint control peptide bound protein complex
Function / homology
Function and homology information


broken chromosome clustering / RecQ family helicase-topoisomerase III complex / G2/M DNA damage checkpoint / HDR through Single Strand Annealing (SSA) / resolution of DNA recombination intermediates / DNA/DNA annealing activity / BRCA1-B complex / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / Processing of DNA double-strand break ends ...broken chromosome clustering / RecQ family helicase-topoisomerase III complex / G2/M DNA damage checkpoint / HDR through Single Strand Annealing (SSA) / resolution of DNA recombination intermediates / DNA/DNA annealing activity / BRCA1-B complex / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / Processing of DNA double-strand break ends / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA geometric change / negative regulation of cell division / phosphorylation-dependent protein binding / telomere maintenance via semi-conservative replication / Y-form DNA binding / telomeric D-loop disassembly / Regulation of TP53 Activity through Phosphorylation / four-way junction helicase activity / homologous recombination / t-circle formation / G-quadruplex DNA binding / DNA double-strand break processing / DNA replication checkpoint signaling / bubble DNA binding / cellular response to hydroxyurea / negative regulation of DNA recombination / cellular response to camptothecin / lateral element / mitotic DNA replication checkpoint signaling / double-strand break repair via classical nonhomologous end joining / double-strand break repair via alternative nonhomologous end joining / regulation of cyclin-dependent protein serine/threonine kinase activity / Impaired BRCA2 binding to PALB2 / protein localization to site of double-strand break / Processive synthesis on the C-strand of the telomere / chromatin-protein adaptor activity / reciprocal meiotic recombination / HDR through Single Strand Annealing (SSA) / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / response to ionizing radiation / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / nuclear chromosome / Resolution of D-loop Structures through Holliday Junction Intermediates / mitotic G2 DNA damage checkpoint signaling / Impaired BRCA2 binding to RAD51 / protein complex oligomerization / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / DNA replication initiation / Presynaptic phase of homologous DNA pairing and strand exchange / chromosome organization / response to X-ray / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / telomere maintenance / DNA helicase activity / replication fork / helicase activity / condensed nuclear chromosome / cellular response to ionizing radiation / male germ cell nucleus / protein serine/threonine kinase activator activity / protein homooligomerization / G2/M DNA damage checkpoint / PML body / double-strand break repair via homologous recombination / Meiotic recombination / HDR through Homologous Recombination (HRR) / nuclear matrix / spindle pole / p53 binding / single-stranded DNA binding / chromosome / actin cytoskeleton / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / DNA damage response / centrosome / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / : / BDHCT (NUC031) domain / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : ...RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / : / BDHCT (NUC031) domain / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / twin BRCT domain / RQC domain / RQC / RQC domain / BRCT domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain / DNA helicase, ATP-dependent, RecQ type / HRDC domain profile. / HRDC domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / HRDC-like superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RecQ-like DNA helicase BLM / DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGlover, J.N.M. / Sun, L. / Edwards, R.A.
Funding support United States, Canada, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)PO1CA092584 United States
Canadian Institutes of Health Research (CIHR)114975 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)Discovery grant 2016-05163 Canada
CitationJournal: Structure / Year: 2017
Title: Structural Insight into BLM Recognition by TopBP1.
Authors: Sun, L. / Huang, Y. / Edwards, R.A. / Yang, S. / Blackford, A.N. / Niedzwiedz, W. / Glover, J.N.M.
History
DepositionDec 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: DNA topoisomerase 2-binding protein 1
C: DNA topoisomerase 2-binding protein 1
D: DNA topoisomerase 2-binding protein 1
E: DNA topoisomerase 2-binding protein 1
F: DNA topoisomerase 2-binding protein 1
G: DNA topoisomerase 2-binding protein 1
H: DNA topoisomerase 2-binding protein 1
L: Bloom Sydrome recQ helicase like protein (BLM)
M: Bloom Sydrome recQ helicase like protein (BLM)
N: Bloom Sydrome recQ helicase like protein (BLM)
O: Bloom Sydrome recQ helicase like protein (BLM)


Theoretical massNumber of molelcules
Total (without water)179,70612
Polymers179,70612
Non-polymers00
Water00
1
A: DNA topoisomerase 2-binding protein 1
E: DNA topoisomerase 2-binding protein 1
L: Bloom Sydrome recQ helicase like protein (BLM)


Theoretical massNumber of molelcules
Total (without water)44,9273
Polymers44,9273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA topoisomerase 2-binding protein 1
F: DNA topoisomerase 2-binding protein 1
M: Bloom Sydrome recQ helicase like protein (BLM)


Theoretical massNumber of molelcules
Total (without water)44,9273
Polymers44,9273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA topoisomerase 2-binding protein 1
G: DNA topoisomerase 2-binding protein 1
N: Bloom Sydrome recQ helicase like protein (BLM)


Theoretical massNumber of molelcules
Total (without water)44,9273
Polymers44,9273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA topoisomerase 2-binding protein 1
H: DNA topoisomerase 2-binding protein 1
O: Bloom Sydrome recQ helicase like protein (BLM)


Theoretical massNumber of molelcules
Total (without water)44,9273
Polymers44,9273
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.164, 96.817, 127.050
Angle α, β, γ (deg.)90.000, 94.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain L
21chain M
12(chain A and (resseq 554:587 or resseq 589:590 or resseq...
22(chain B and (resseq 554:587 or resseq 589:590 or resseq...
32(chain C and (resseq 554:587 or resseq 589:590 or resseq...
42(chain D and (resseq 554:587 or resseq 589:590 or resseq...
52(chain E and (resseq 554:587 or resseq 589:590 or resseq...
62(chain F and (resseq 554:587 or resseq 589:590 or resseq...
72(chain G and (resseq 554:587 or resseq 589:590 or resseq...
82(chain H and (resseq 554:587 or resseq 589:590 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEPROPROchain LLI300 - 3054 - 9
211PHEPHEPROPROchain MMJ300 - 3054 - 9
112GLYGLYSERSER(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 5878 - 41
122PROPROSERSER(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA589 - 59043 - 44
132ILEILESERSER(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA592 - 65546 - 109
142PHEPHEPHEPHE(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA656110
152GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
162GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
172GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
182GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
192GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
1102GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
1112GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
1122GLYGLYASNASN(chain A and (resseq 554:587 or resseq 589:590 or resseq...AA554 - 7438 - 197
212GLYGLYSERSER(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 5878 - 41
222PROPROSERSER(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB589 - 59043 - 44
232ILEILESERSER(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB592 - 65546 - 109
242PHEPHEPHEPHE(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB656110
252GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
262GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
272GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
282GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
292GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
2102GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
2112GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
2122GLYGLYASNASN(chain B and (resseq 554:587 or resseq 589:590 or resseq...BB554 - 7438 - 197
312GLYGLYSERSER(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 5878 - 41
322PROPROSERSER(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC589 - 59043 - 44
332ILEILESERSER(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC592 - 65546 - 109
342PHEPHEPHEPHE(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC656110
352GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
362GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
372GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
382GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
392GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
3102GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
3112GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
3122GLYGLYASNASN(chain C and (resseq 554:587 or resseq 589:590 or resseq...CC554 - 7438 - 197
412GLYGLYSERSER(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 5878 - 41
422PROPROSERSER(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD589 - 59043 - 44
432ILEILESERSER(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD592 - 65546 - 109
442PHEPHEPHEPHE(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD656110
452GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
462GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
472GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
482GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
492GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
4102GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
4112GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
4122GLYGLYASNASN(chain D and (resseq 554:587 or resseq 589:590 or resseq...DD554 - 7438 - 197
512GLYGLYSERSER(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE554 - 5878 - 41
522PROPROSERSER(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE589 - 59043 - 44
532ILEILESERSER(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE592 - 65546 - 109
542PHEPHEPHEPHE(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE656110
552GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
562GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
572GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
582GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
592GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
5102GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
5112GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
5122GLUGLUASNASN(chain E and (resseq 554:587 or resseq 589:590 or resseq...EE553 - 7437 - 197
612GLYGLYSERSER(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF554 - 5878 - 41
622PROPROSERSER(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF589 - 59043 - 44
632ILEILESERSER(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF592 - 65546 - 109
642PHEPHEPHEPHE(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF656110
652GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
662GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
672GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
682GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
692GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
6102GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
6112GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
6122GLUGLUASNASN(chain F and (resseq 554:587 or resseq 589:590 or resseq...FF553 - 7437 - 197
712GLYGLYSERSER(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG554 - 5878 - 41
722PROPROSERSER(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG589 - 59043 - 44
732ILEILESERSER(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG592 - 65546 - 109
742PHEPHEPHEPHE(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG656110
752GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
762GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
772GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
782GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
792GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
7102GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
7112GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
7122GLUGLUASNASN(chain G and (resseq 554:587 or resseq 589:590 or resseq...GG553 - 7437 - 197
812GLYGLYSERSER(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH554 - 5878 - 41
822PROPROSERSER(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH589 - 59043 - 44
832ILEILESERSER(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH592 - 65546 - 109
842PHEPHEPHEPHE(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH656110
852GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
862GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
872GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
882GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
892GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
8102GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
8112GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197
8122GLUGLUASNASN(chain H and (resseq 554:587 or resseq 589:590 or resseq...HH553 - 7437 - 197

NCS ensembles :
ID
1
2

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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: 21694.020 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: BRCT4,5 domains, residue 553-743 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Topbp1, Kiaa0259 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZQF0
#2: Protein/peptide
Bloom Sydrome recQ helicase like protein (BLM)


Mass: 1538.544 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: phosphopeptide, residue 300-312 / Source: (synth.) Homo sapiens (human) / References: UniProt: P54132*PLUS
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 0.1M Sodium Citrate 24% PEG8000

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 71934 / % possible obs: 98.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 54.87 Å2 / Rmerge(I) obs: 0.126 / Net I/av σ(I): 16.6 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.6-2.694.30.8231.90.896193.1
2.69-2.850.8010.908196.9
2.8-2.935.70.6010.959198.6
2.93-3.086.10.4760.972199.6
3.08-3.286.60.3430.984199.9
3.28-3.536.90.2380.9911100
3.53-3.887.10.1620.9941100
3.88-4.457.20.1130.9961100
4.45-5.67.20.0920.9971100
5.6-5070.0640.998199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.69 Å48.49 Å
Translation6.69 Å48.49 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UEN

3uen


Resolution: 2.6→47.874 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 34.88
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 3633 5.07 %Random selection
Rwork0.2193 ---
obs0.2211 71624 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 317.31 Å2 / Biso mean: 112.2152 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: final / Resolution: 2.6→47.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11899 0 0 0 11899
Num. residues----1551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312134
X-RAY DIFFRACTIONf_angle_d0.54616514
X-RAY DIFFRACTIONf_chiral_restr0.0481981
X-RAY DIFFRACTIONf_plane_restr0.0052088
X-RAY DIFFRACTIONf_dihedral_angle_d9.9067280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11L52X-RAY DIFFRACTION4.468TORSIONAL
12M52X-RAY DIFFRACTION4.468TORSIONAL
21A6443X-RAY DIFFRACTION4.468TORSIONAL
22B6443X-RAY DIFFRACTION4.468TORSIONAL
23C6443X-RAY DIFFRACTION4.468TORSIONAL
24D6443X-RAY DIFFRACTION4.468TORSIONAL
25E6443X-RAY DIFFRACTION4.468TORSIONAL
26F6443X-RAY DIFFRACTION4.468TORSIONAL
27G6443X-RAY DIFFRACTION4.468TORSIONAL
28H6443X-RAY DIFFRACTION4.468TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5998-2.6340.35311150.36232080219579
2.634-2.67010.35761010.34212474257593
2.6701-2.70820.37451280.33262518264694
2.7082-2.74860.36881290.32912550267996
2.7486-2.79160.41091370.31772588272597
2.7916-2.83740.34471460.31582567271397
2.8374-2.88630.34111690.31542589275897
2.8863-2.93870.36471360.30712612274899
2.9387-2.99530.37011410.27652627276899
2.9953-3.05640.30231310.26352647277899
3.0564-3.12280.26181600.24232624278499
3.1228-3.19550.30051230.240127042827100
3.1955-3.27540.29191420.254126472789100
3.2754-3.36390.24711730.240526282801100
3.3639-3.46290.27741050.230626692774100
3.4629-3.57460.26521300.23912666279699
3.5746-3.70230.26131390.23392662280199
3.7023-3.85050.21641470.205626462793100
3.8505-4.02560.2391490.200226552804100
4.0256-4.23780.24711360.199126932829100
4.2378-4.50310.22871570.193326412798100
4.5031-4.85050.2131540.171526882842100
4.8505-5.3380.22061310.179626942825100
5.338-6.10910.22641600.208526742834100
6.1091-7.69160.23921490.204926972846100
7.6916-47.88210.21781450.16672751289699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8942-1.24710.52823.6609-0.09712.245-0.00080.06940.507-0.04470.0299-0.5368-0.1820.21520.06980.26030.04890.0550.23460.00051.052655.915386.090159.5066
24.4223-2.09630.19086.6001-1.64820.63760.35650.5811-0.1437-1.6731-0.18180.32150.27240.0334-0.11590.58490.02380.25770.2810.01140.903756.183580.652452.4517
31.76-2.42250.33183.9144-2.51787.5018-0.3537-0.16411.06740.0089-0.3446-0.66-0.48890.39470.62650.33890.00040.00990.4093-0.1371.270962.204784.24966.0729
45.6211.19721.28834.22091.51380.68380.0157-0.3961-0.34980.78960.2034-1.07980.2110.1584-0.22940.30750.1187-0.18540.1726-0.04460.655849.756580.777266.9644
52.50020.48470.13878.6506-4.28213.582-0.16590.05070.5924-0.80760.042-0.1529-0.7123-0.04020.06210.35460.0343-0.01510.0632-0.07380.57647.259788.543956.8938
62.13670.7614-1.31862.7395-3.02574.3519-0.1119-0.0732-0.44170.00470.0382-0.3194-0.0225-0.19820.07390.33350.03520.02050.1915-0.09790.952440.047785.956562.4699
72.8486-1.37781.6451.48081.53377.6097-0.13090.50960.3248-0.3777-00.3031-0.2315-0.36120.06470.3660.0187-0.11720.40560.10221.38126.684181.234853.6861
87.0728-0.1594-0.79844.93472.67821.7139-0.4771.45020.6099-1.1650.21970.5417-0.3003-0.27430.09940.531-0.0907-0.14240.56120.13261.073527.879279.607450.2089
92.91941.6039-0.92623.96060.44041.7571-0.42010.96020.3941-0.66260.32890.3613-0.6106-0.18280.06550.5781-0.0288-0.14540.65010.22971.596921.83283.641948.4419
102.78420.4409-0.42651.39631.45781.8244-0.22150.55630.9473-0.29340.24961.1263-0.5027-0.55560.00020.45290.00250.00020.50540.19931.652121.900286.797756.8389
114.8961-4.31760.54748.11390.40525.2841-0.02230.060.06090.18260.00410.6818-0.6606-0.45320.00470.55370.07110.22440.39040.04181.644120.2986.43963.9553
122.76344.9487-0.46779.2515-1.2847.0430.02410.40720.4325-0.76610.4535-1.4263-0.33580.1529-0.42210.58710.0995-0.02830.5214-0.02541.4519110.112990.6547-7.3222
137.2632-1.32662.35940.88230.0982.8902-0.0354-0.10760.0817-0.02520.00720.16840.0127-0.1520.00940.6370.0163-0.06720.4637-0.01231.45297.166891.3536-3.0768
148.06214.14164.62754.72932.04836.6029-0.78720.81620.605-1.52030.18510.64980.0227-0.90090.49650.9386-0.0859-0.31651.1561-0.16921.410875.233585.1482-18.8293
155.6684-0.61612.49867.906-2.36515.9169-0.67830.24080.8964-0.07030.60850.5868-0.7322-0.82250.0360.61990.0127-0.15140.67060.14611.645476.213695.0319-7.8481
160.4874-1.54461.74314.8993-5.52936.2393-0.25350.35931.36190.94150.39791.3111-1.3535-1.054-0.12290.6720.11120.02250.70070.07141.957274.308794.23640.4156
170.4233-0.4587-0.24463.8003-0.68890.4289-0.0287-0.1286-0.35170.6377-0.2046-0.8460.00750.25120.10410.4762-0.0685-0.18050.3338-0.03021.66596.939972.53870.9434
182.12991.8638-0.98641.8707-1.05762.169-0.0983-0.0756-0.37070.0471-0.2158-0.39090.2006-0.07430.20540.4169-0.0523-0.01020.4525-0.02871.685913.132371.425260.7048
194.3646-2.2469-1.44077.10243.45371.71390.19470.2810.6071-0.72960.2434-1.2726-0.33050.11-0.33280.4091-0.00350.0080.32250.01381.40150.697974.878759.8738
201.06361.1414-0.35914.2492-0.67122.78540.0881-0.0902-0.43380.5679-0.1614-0.21710.20050.05550.1460.3674-0.0506-0.01660.19110.00021.2265-1.825767.177769.9783
211.6439-2.9445-0.2415.4220.11841.9927-0.0297-0.0652-0.3628-0.03950.00890.04280.0593-0.21160.08060.33520.0073-0.09120.2767-0.00231.3082-14.287772.539568.9708
229.59651.8872-3.52685.1197-3.64869.8278-0.4093-2.5716-0.01551.4873-0.29710.7369-0.57550.1340.56170.6470.1110.23150.9782-0.15791.0144-27.762178.367181.7609
231.4548-0.6661.11682.33420.81111.7215-0.1794-0.584-0.8393-0.00630.21321.05550.5984-0.446-0.16630.4763-0.01830.01890.38830.22491.4598-26.84168.247971.0089
245.95732.40121.27022.41180.46934.77150.0128-0.4505-0.52520.0938-0.3017-0.01670.3236-0.45890.26130.4238-0.0302-0.23270.43890.01121.5502-28.780869.230462.6888
254.9613-3.546-2.12146.866-0.63526.009-0.4475-0.1924-0.17090.80770.4179-1.47950.18190.4133-0.02320.6335-0.0067-0.31920.44270.04531.550460.630977.44933.9365
263.6792-3.2946-0.71755.1421-0.85735.4288-0.3717-0.9790.33271.92390.6044-1.6558-0.39650.6664-0.16060.9759-0.0111-0.46560.6486-0.00861.526961.100983.030410.8107
270.60152.0409-1.53547.0261-5.08884.0916-0.0868-0.2157-0.27680.1748-0.7752-1.00830.02361.06550.81460.6066-0.0571-0.05980.78340.01741.939366.94379.2076-2.6657
289.3663-7.6353-1.62666.53812.33674.52440.06090.7487-1.0417-0.2572-0.1835-0.6743-0.42610.32930.15980.5885-0.1687-0.11210.5973-0.0581.32954.363482.7435-3.4347
297.44760.8992-1.00452.19231.75592.1959-0.19-0.1812-0.090.69620.3567-0.88290.3578-0.315-0.13590.58220.0305-0.13870.43940.02531.012752.048875.00136.7039
306.40031.4081-3.26681.37851.45816.1206-0.05920.67010.4452-0.0655-0.042-0.50340.2145-0.32620.08420.551-0.0989-0.16360.45030.01221.3941.397579.98811.8749
317.8228-0.5906-2.95697.74471.48045.587-0.2295-0.9044-0.2470.1842-0.1296-0.7308-0.01110.28230.3650.6044-0.0174-0.23960.5315-0.02360.937537.390780.981810.9466
325.0861-0.4136-3.03737.97942.72576.9202-0.1737-2.81990.1671.859-0.16370.57880.02430.64840.31120.82870.0812-0.0261.2736-0.02970.879626.058885.905818.0536
334.237-2.3534-4.88284.7018-0.67589.34510.2172-2.53860.30971.09490.8756-0.0429-0.20380.8438-1.20820.6672-0.1448-0.24541.2223-0.03110.926625.570784.477415.9145
346.1353-0.3515-3.32957.73860.022.3891-0.3094-0.4486-1.6379-0.10630.30320.92411.1148-1.06810.05670.5973-0.1301-0.23220.70910.19921.211927.394875.21657.7914
358.5595-0.8553-2.53792.34251.09311.98360.15410.5093-1.5442-1.01640.02671.92560.8778-0.9549-0.13260.8887-0.0402-0.40410.61640.03851.224625.110776.84540.0817
360.8316-0.3760.01634.2625-0.68631.18480.2186-0.1248-0.14460.4391-0.0352-0.80290.2090.2735-0.11870.40240.0208-0.09420.0522-0.04591.159849.294258.551561.3935
372.05111.0684-0.49675.0243-0.35341.3417-0.17250.87850.07-1.56950.44680.74210.5376-0.2996-0.06471.3278-0.1043-0.25820.5628-0.04390.683342.874959.737434.5915
388.8512-0.2118-0.91696.7486-2.61045.85280.2851-0.2086-0.0992-0.13360.0681-0.10550.02940.0359-0.31190.6302-0.0419-0.20130.4083-0.05761.095102.955167.22810.2207
393.42221.5893-2.53886.1358-0.55131.95990.18041.9571-0.6813-2.1410.75280.43581.7405-0.8395-0.81152.4994-0.1065-0.50071.6075-0.21981.191698.14565.5513-27.4422
400.43430.3335-0.01113.5443-1.01420.68620.1052-0.02680.2675-0.1796-0.0107-0.4187-0.05040.1630.00990.467-0.00310.0460.0105-0.18451.71550.153797.19765.1034
410.45520.1844-0.02270.6432-0.44430.33270.1721-1.56510.65611.2648-0.29750.37-0.4435-0.390.22092.0602-0.36280.11.394-0.56341.3292-6.75696.972591.933
427.35540.9621-1.32016.9015-1.13181.97230.2236-0.2180.26910.01940.092-1.0665-0.24210.1473-0.30020.69050.0122-0.0870.4445-0.06471.234754.1048104.99081.5913
433.1655-2.44170.242.7116-2.43636.8253-0.2255-2.2820.77183.03010.3127-0.4335-0.1356-0.6727-0.08312.9431-0.1337-0.28751.8189-0.37231.458348.2054105.037928.4432
441.5626-1.1104-0.63831.0661-0.0891.9204-0.17480.4502-0.3055-0.35040.2557-0.00820.1401-0.09-0.04691.5484-0.092-0.02831.59580.55731.62124.468187.686141.0482
454.2629-0.09810.59411.41670.16522.74430.01350.1922-0.4316-0.14730.1246-0.18280.17970.015-0.11642.0182-0.1974-0.09271.8840.4381.437178.492895.1471-22.4661
467.02372.23413.46213.13333.22553.56920.2616-0.3661.12520.1485-0.15050.1368-1.099-0.6961-0.10091.9110.2146-0.26591.5070.45671.9149-27.832369.615286.3881
474.1514-0.8935.36383.9284-2.30117.433-0.45710.6020.0860.53620.5033-0.0342-0.6065-0.8118-0.01911.2679-0.0424-0.51921.40720.5061.071834.600874.812823.7848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 554 through 567 )A554 - 567
2X-RAY DIFFRACTION2chain 'A' and (resid 568 through 581 )A568 - 581
3X-RAY DIFFRACTION3chain 'A' and (resid 582 through 595 )A582 - 595
4X-RAY DIFFRACTION4chain 'A' and (resid 596 through 611 )A596 - 611
5X-RAY DIFFRACTION5chain 'A' and (resid 612 through 625 )A612 - 625
6X-RAY DIFFRACTION6chain 'A' and (resid 626 through 647 )A626 - 647
7X-RAY DIFFRACTION7chain 'A' and (resid 648 through 661 )A648 - 661
8X-RAY DIFFRACTION8chain 'A' and (resid 662 through 687 )A662 - 687
9X-RAY DIFFRACTION9chain 'A' and (resid 688 through 705 )A688 - 705
10X-RAY DIFFRACTION10chain 'A' and (resid 706 through 730 )A706 - 730
11X-RAY DIFFRACTION11chain 'A' and (resid 731 through 743 )A731 - 743
12X-RAY DIFFRACTION12chain 'B' and (resid 554 through 581 )B554 - 581
13X-RAY DIFFRACTION13chain 'B' and (resid 582 through 673 )B582 - 673
14X-RAY DIFFRACTION14chain 'B' and (resid 674 through 693 )B674 - 693
15X-RAY DIFFRACTION15chain 'B' and (resid 694 through 730 )B694 - 730
16X-RAY DIFFRACTION16chain 'B' and (resid 731 through 743 )B731 - 743
17X-RAY DIFFRACTION17chain 'C' and (resid 554 through 581 )C554 - 581
18X-RAY DIFFRACTION18chain 'C' and (resid 582 through 595 )C582 - 595
19X-RAY DIFFRACTION19chain 'C' and (resid 596 through 611 )C596 - 611
20X-RAY DIFFRACTION20chain 'C' and (resid 612 through 625 )C612 - 625
21X-RAY DIFFRACTION21chain 'C' and (resid 626 through 673 )C626 - 673
22X-RAY DIFFRACTION22chain 'C' and (resid 674 through 693 )C674 - 693
23X-RAY DIFFRACTION23chain 'C' and (resid 694 through 730 )C694 - 730
24X-RAY DIFFRACTION24chain 'C' and (resid 731 through 743 )C731 - 743
25X-RAY DIFFRACTION25chain 'D' and (resid 554 through 567 )D554 - 567
26X-RAY DIFFRACTION26chain 'D' and (resid 568 through 581 )D568 - 581
27X-RAY DIFFRACTION27chain 'D' and (resid 582 through 595 )D582 - 595
28X-RAY DIFFRACTION28chain 'D' and (resid 596 through 611 )D596 - 611
29X-RAY DIFFRACTION29chain 'D' and (resid 612 through 625 )D612 - 625
30X-RAY DIFFRACTION30chain 'D' and (resid 626 through 652 )D626 - 652
31X-RAY DIFFRACTION31chain 'D' and (resid 653 through 673 )D653 - 673
32X-RAY DIFFRACTION32chain 'D' and (resid 674 through 689 )D674 - 689
33X-RAY DIFFRACTION33chain 'D' and (resid 690 through 699 )D690 - 699
34X-RAY DIFFRACTION34chain 'D' and (resid 700 through 730 )D700 - 730
35X-RAY DIFFRACTION35chain 'D' and (resid 731 through 743 )D731 - 743
36X-RAY DIFFRACTION36chain 'E' and (resid 553 through 647 )E553 - 647
37X-RAY DIFFRACTION37chain 'E' and (resid 648 through 743 )E648 - 743
38X-RAY DIFFRACTION38chain 'F' and (resid 553 through 637 )F553 - 637
39X-RAY DIFFRACTION39chain 'F' and (resid 638 through 743 )F638 - 743
40X-RAY DIFFRACTION40chain 'G' and (resid 553 through 647 )G553 - 647
41X-RAY DIFFRACTION41chain 'G' and (resid 648 through 743 )G648 - 743
42X-RAY DIFFRACTION42chain 'H' and (resid 553 through 647 )H553 - 647
43X-RAY DIFFRACTION43chain 'H' and (resid 648 through 743 )H648 - 743
44X-RAY DIFFRACTION44chain 'L' and (resid 300 through 305 )L300 - 305
45X-RAY DIFFRACTION45chain 'M' and (resid 300 through 305 )M300 - 305
46X-RAY DIFFRACTION46chain 'N' and (resid 300 through 303 )N300 - 303
47X-RAY DIFFRACTION47chain 'O' and (resid 300 through 309 )O300 - 309

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