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- PDB-8xrg: The crystal structure of AsfvTopII ATPase domain in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8xrg
TitleThe crystal structure of AsfvTopII ATPase domain in complex with ADP
ComponentsDNA topoisomerase 2
KeywordsREPLICATION / Topoisomerases 2 / Complex / ADP
Function / homology
Function and homology information


sister chromatid segregation / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / host cell cytoplasm / DNA binding / ATP binding / metal ion binding
Similarity search - Function
: / 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 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 / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / DNA topoisomerase, type IIA-like domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus BA71V
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsYang, J. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: The crystal structure of AsfvTopII ATPase domain in complex with ADP
Authors: Yang, J. / Gan, J.H.
History
DepositionJan 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0104
Polymers45,4641
Non-polymers5463
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.256, 85.256, 209.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-726-

HOH

21A-730-

HOH

31A-771-

HOH

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Components

#1: Protein DNA topoisomerase 2 / DNA topoisomerase II


Mass: 45463.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Gene: TOP, Ba71V-112, P1192R / Production host: Escherichia coli (E. coli)
References: UniProt: Q00942, DNA topoisomerase (ATP-hydrolysing)
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium phosphate dibasic, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979191 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.61→60.35 Å / Num. obs: 59466 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.027 / Rrim(I) all: 0.092 / Χ2: 0.93 / Net I/σ(I): 17.4 / Num. measured all: 661408
Reflection shellResolution: 1.61→1.69 Å / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 1.29 / Num. measured all: 80434 / Num. unique obs: 8497 / CC1/2: 0.63 / Rpim(I) all: 0.43 / Rrim(I) all: 1.361 / Χ2: 0.69 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
XDSdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→42.72 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 2927 4.93 %
Rwork0.1856 --
obs0.1866 59352 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2936 0 33 200 3169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083051
X-RAY DIFFRACTIONf_angle_d1.0824156
X-RAY DIFFRACTIONf_dihedral_angle_d15.3261072
X-RAY DIFFRACTIONf_chiral_restr0.068489
X-RAY DIFFRACTIONf_plane_restr0.013519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.28731360.27562633X-RAY DIFFRACTION100
1.63-1.660.28071180.2542654X-RAY DIFFRACTION100
1.66-1.690.29991350.2452634X-RAY DIFFRACTION100
1.69-1.720.26781450.23212622X-RAY DIFFRACTION100
1.72-1.760.27621360.21672656X-RAY DIFFRACTION100
1.76-1.80.24431270.21572650X-RAY DIFFRACTION100
1.8-1.840.23311410.20462645X-RAY DIFFRACTION100
1.84-1.890.23441440.19652640X-RAY DIFFRACTION100
1.89-1.940.21441480.19682651X-RAY DIFFRACTION100
1.94-1.990.23171560.19222636X-RAY DIFFRACTION100
1.99-2.060.23831280.18442667X-RAY DIFFRACTION100
2.06-2.130.24591600.1872659X-RAY DIFFRACTION100
2.13-2.220.22881180.1872669X-RAY DIFFRACTION100
2.22-2.320.20651310.18512695X-RAY DIFFRACTION100
2.32-2.440.20251360.18692697X-RAY DIFFRACTION100
2.44-2.590.21661410.18392703X-RAY DIFFRACTION100
2.59-2.790.21031280.19412710X-RAY DIFFRACTION100
2.79-3.070.21661380.19482730X-RAY DIFFRACTION100
3.07-3.520.18211460.17732748X-RAY DIFFRACTION100
3.52-4.430.1711550.1562779X-RAY DIFFRACTION100
4.43-42.720.18221600.17742947X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 32.3645 Å / Origin y: 12.532 Å / Origin z: -7.4374 Å
111213212223313233
T0.2053 Å2-0.0104 Å2-0.0138 Å2-0.1115 Å20.003 Å2--0.1426 Å2
L1.0101 °2-0.008 °2-0.4904 °2-0.8122 °20.1956 °2--0.9099 °2
S-0.0087 Å °0.0612 Å °0.0146 Å °-0.0676 Å °0.0129 Å °-0.0253 Å °-0.1381 Å °-0.0101 Å °0 Å °
Refinement TLS groupSelection details: all

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