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- PDB-7zbg: Human Topoisomerase II Beta ATPase ADP -

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Basic information

Entry
Database: PDB / ID: 7zbg
TitleHuman Topoisomerase II Beta ATPase ADP
ComponentsDNA topoisomerase 2-beta
KeywordsDNA BINDING PROTEIN / DNA Topoisomerase II Beta / Human / ATPase Domain / TOP2B
Function / homology
Function and homology information


positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / positive regulation of double-strand break repair via nonhomologous end joining / cellular response to ATP / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / axonogenesis / B cell differentiation / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-ITH / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLing, E.M. / Basle, A. / Cowell, I.G. / Blower, T.R. / Austin, C.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193.
Authors: Ling, E.M. / Basle, A. / Cowell, I.G. / van den Berg, B. / Blower, T.R. / Austin, C.A.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7868
Polymers45,6661
Non-polymers1,1207
Water90150
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,57116
Polymers91,3312
Non-polymers2,24014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7810 Å2
ΔGint-140 kcal/mol
Surface area31140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.400, 103.400, 67.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA topoisomerase 2-beta / DNA topoisomerase II / beta isozyme


Mass: 45665.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP2B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q02880, DNA topoisomerase (ATP-hydrolysing)

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Non-polymers , 5 types, 57 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ITH / 4-[(2S,3R)-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione


Mass: 284.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate, 0.1 M bis tris (pH 5.5), 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.3→53.714 Å / Num. obs: 18666 / % possible obs: 99.8 % / Redundancy: 19.2 % / CC1/2: 0.996 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1821 / CC1/2: 0.565

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Processing

Software
NameVersionClassification
REFMAC5.8.0326refinement
xia2data reduction
XDSdata reduction
Cootmodel building
MolProbitymodel building
pointlessdata scaling
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QFO

7qfo


Resolution: 2.3→53.714 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.481 / SU ML: 0.202 / Cross valid method: FREE R-VALUE / ESU R: 0.342 / ESU R Free: 0.252
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2593 983 5.268 %
Rwork0.1972 17678 -
all0.201 --
obs-18661 99.727 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.233 Å2
Baniso -1Baniso -2Baniso -3
1-0.456 Å20.228 Å20 Å2
2--0.456 Å2-0 Å2
3----1.479 Å2
Refinement stepCycle: LAST / Resolution: 2.3→53.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 68 50 3027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123046
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162880
X-RAY DIFFRACTIONr_angle_refined_deg1.821.6384111
X-RAY DIFFRACTIONr_angle_other_deg0.5871.5736656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3265363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.19822.72733
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1710.189557
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.4310116
X-RAY DIFFRACTIONr_chiral_restr0.0830.2457
X-RAY DIFFRACTIONr_chiral_restr_other0.0030.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_nbd_refined0.2310.2527
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.22566
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21443
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2950.220
X-RAY DIFFRACTIONr_nbd_other0.1920.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.29
X-RAY DIFFRACTIONr_mcbond_it4.5424.0791452
X-RAY DIFFRACTIONr_mcbond_other4.5274.0761451
X-RAY DIFFRACTIONr_mcangle_it6.3936.1061812
X-RAY DIFFRACTIONr_mcangle_other6.3926.1081813
X-RAY DIFFRACTIONr_scbond_it5.7634.5991594
X-RAY DIFFRACTIONr_scbond_other5.7614.5991595
X-RAY DIFFRACTIONr_scangle_it8.1086.6392298
X-RAY DIFFRACTIONr_scangle_other8.1066.6392299
X-RAY DIFFRACTIONr_lrange_it10.5950.653276
X-RAY DIFFRACTIONr_lrange_other10.55450.7543274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.245600.25213040.25213640.9460.9541000.24
2.36-2.4240.271630.21912580.22113210.9410.9651000.198
2.424-2.4940.327680.23412270.23912950.9190.9611000.209
2.494-2.5710.275670.20811920.21212590.9530.9711000.182
2.571-2.6550.305430.22711650.2312080.9340.9651000.196
2.655-2.7480.285360.25411390.25511780.9350.95299.74530.226
2.748-2.8510.293760.20610730.21111490.9440.9731000.175
2.851-2.9680.335580.19610300.20410880.9260.9761000.168
2.968-3.0990.27610.18610100.19110710.9480.9771000.159
3.099-3.250.251690.189380.18510070.9610.9791000.157
3.25-3.4250.279390.2049260.2079700.9450.97499.48450.178
3.425-3.6320.24600.2018430.2039060.9670.97799.66890.176
3.632-3.8810.24500.2017860.2048550.9630.97697.77780.174
3.881-4.190.226520.1717520.1758210.9720.98197.92940.15
4.19-4.5870.222430.1476900.1517330.9730.9871000.138
4.587-5.1240.221350.1626630.1656980.9750.9861000.155
5.124-5.9080.313310.2015620.2075930.9450.9811000.189
5.908-7.2140.212260.1724970.1745230.9750.9831000.161
7.214-10.1110.202240.1983890.1984130.9750.9791000.198
10.111-53.7140.356220.2632340.2692580.9440.96299.22480.284

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