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- PDB-7qfo: Human Topoisomerase II Beta ATPase AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7qfo
TitleHuman Topoisomerase II Beta ATPase AMPPNP
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) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / 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) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / 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 / metal ion binding / nucleus / cytosol
Similarity search - Function
DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / 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 ...DTHCT / DTHCT (NUC029) region / DNA topoisomerase 2, TOPRIM domain / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / 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
ALANINE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DNA topoisomerase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionDec 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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

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Assembly

Deposited unit
A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2854
Polymers45,6661
Non-polymers6203
Water1,78399
1
A: DNA topoisomerase 2-beta
hetero molecules

A: DNA topoisomerase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5708
Polymers91,3312
Non-polymers1,2396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area6970 Å2
ΔGint-41 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.021, 84.021, 127.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#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 (E. coli)
References: UniProt: Q02880, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCTP (pH 7.0), 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→59.42 Å / Num. obs: 36646 / % possible obs: 100 % / Redundancy: 48 % / CC1/2: 1 / Net I/σ(I): 23.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 50.9 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2300 / CC1/2: 0.568 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
xia2data reduction
pointlessdata scaling
Cootmodel building
MolProbitymodel building
Aimlessdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZXM

1zxm


Resolution: 1.9→59.412 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.167 / SU B: 3.97 / SU ML: 0.111 / Average fsc free: 0.8965 / Average fsc work: 0.91 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2318 1769 4.838 %
Rwork0.1927 34798 -
all0.195 --
obs-36567 99.975 %
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: 42.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.224 Å2-0 Å2-0 Å2
2--0.224 Å2-0 Å2
3----0.447 Å2
Refinement stepCycle: LAST / Resolution: 1.9→59.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 37 99 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133136
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163018
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.6474232
X-RAY DIFFRACTIONr_angle_other_deg1.3431.596975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4285379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07624.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73315589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2061511
X-RAY DIFFRACTIONr_chiral_restr0.0820.2411
X-RAY DIFFRACTIONr_chiral_restr_other0.3690.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined0.2110.2552
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22680
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21489
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2113
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.216
X-RAY DIFFRACTIONr_nbd_other0.1970.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1370.28
X-RAY DIFFRACTIONr_mcbond_it3.6424.0991519
X-RAY DIFFRACTIONr_mcbond_other3.6444.0961518
X-RAY DIFFRACTIONr_mcangle_it4.5416.1191894
X-RAY DIFFRACTIONr_mcangle_other4.546.1221895
X-RAY DIFFRACTIONr_scbond_it4.6214.6091616
X-RAY DIFFRACTIONr_scbond_other4.624.6081616
X-RAY DIFFRACTIONr_scangle_it6.946.6692337
X-RAY DIFFRACTIONr_scangle_other6.9386.6692338
X-RAY DIFFRACTIONr_lrange_it8.28846.5073373
X-RAY DIFFRACTIONr_lrange_other8.29346.4593364
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
1.9-1.9490.321200.28925330.29126540.740.74999.96230.281
1.949-2.0030.3021190.27524770.27625980.8340.81999.9230.26
2.003-2.0610.3171380.25123720.25525120.8360.87299.92040.229
2.061-2.1240.2581250.24223250.24324500.9060.8951000.216
2.124-2.1940.2761190.22222440.22523640.8950.90999.95770.192
2.194-2.2710.2911050.2122040.21423090.8840.9241000.18
2.271-2.3560.2751180.20920880.21322070.9050.92499.95470.175
2.356-2.4520.2591050.19220490.19621540.9280.9431000.161
2.452-2.5610.234950.18619550.18820510.9390.9599.95120.156
2.561-2.6860.3181020.20718750.21219770.8950.9371000.175
2.686-2.8310.279870.21618150.21919020.910.9321000.184
2.831-3.0020.261750.20817210.2117960.9220.9321000.182
3.002-3.2090.259910.21915820.22216730.9070.9261000.197
3.209-3.4650.245810.21715010.21915820.9380.9341000.199
3.465-3.7940.24690.20114010.20214700.9430.9551000.187
3.794-4.240.198560.16512810.16713370.9620.9691000.154
4.24-4.8920.144490.14511390.14511880.980.9791000.133
4.892-5.9810.176440.159850.15110290.970.9791000.139
5.981-8.4160.165430.1577800.1578230.9660.9741000.147
8.416-59.4120.187280.1694700.174980.9740.9671000.154

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