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- PDB-8xrf: The crystal structure of AsfvTopII in complex with G-DNA -

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Basic information

Entry
Database: PDB / ID: 8xrf
TitleThe crystal structure of AsfvTopII in complex with G-DNA
Components
  • DNA (52-MER)
  • DNA topoisomerase 2
KeywordsREPLICATION / Topoisomerase / complex / DNA
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
DNA / DNA (> 10) / DNA topoisomerase 2
Similarity search - Component
Biological speciesAfrican swine fever virus BA71V
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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 in complex with G-DNA
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

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 2
B: DNA topoisomerase 2
C: DNA (52-MER)
D: DNA (52-MER)
E: DNA (52-MER)
F: DNA (52-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,78411
Polymers244,6626
Non-polymers1225
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.770, 126.410, 135.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA topoisomerase 2 / DNA topoisomerase II


Mass: 90286.617 Da / Num. of mol.: 2
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: DNA chain
DNA (52-MER)


Mass: 16022.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus BA71V / Production host: chemical production metagenome (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 40% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.94→31.86 Å / Num. obs: 50298 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.1 / Rrim(I) all: 0.255 / Χ2: 1 / Net I/σ(I): 5.9 / Num. measured all: 327604
Reflection shellResolution: 2.94→3.02 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.245 / Num. measured all: 25249 / Num. unique obs: 3661 / CC1/2: 0.609 / Rpim(I) all: 0.51 / Rrim(I) all: 1.346 / Χ2: 0.86 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
xia2data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→31.86 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2626 2416 4.81 %
Rwork0.2177 --
obs0.2199 50242 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12344 1038 5 3 13390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413929
X-RAY DIFFRACTIONf_angle_d0.86419043
X-RAY DIFFRACTIONf_dihedral_angle_d19.7675249
X-RAY DIFFRACTIONf_chiral_restr0.0532090
X-RAY DIFFRACTIONf_plane_restr0.012249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-30.31511560.30382725X-RAY DIFFRACTION100
3-3.070.29871420.30122773X-RAY DIFFRACTION100
3.07-3.140.35981380.30052791X-RAY DIFFRACTION100
3.14-3.210.36631160.28392785X-RAY DIFFRACTION100
3.21-3.30.3041270.26312814X-RAY DIFFRACTION100
3.3-3.40.2721490.25192765X-RAY DIFFRACTION100
3.4-3.510.33761360.24732800X-RAY DIFFRACTION100
3.51-3.630.3041160.23442826X-RAY DIFFRACTION100
3.63-3.780.26991400.2342800X-RAY DIFFRACTION100
3.78-3.950.25761270.20272829X-RAY DIFFRACTION100
3.95-4.160.28351280.20252807X-RAY DIFFRACTION100
4.16-4.420.22861220.19122823X-RAY DIFFRACTION100
4.42-4.760.21071340.17882828X-RAY DIFFRACTION100
4.76-5.240.23011520.18862821X-RAY DIFFRACTION100
5.24-5.990.24181440.21282867X-RAY DIFFRACTION100
5.99-7.530.28612190.22652785X-RAY DIFFRACTION100
7.53-31.860.2221700.19082987X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.5347 Å / Origin y: 28.1195 Å / Origin z: 30.5115 Å
111213212223313233
T0.3852 Å20.0333 Å2-0.0292 Å2-0.3984 Å2-0.0745 Å2--0.425 Å2
L0.7639 °2-0.0294 °20.2427 °2-0.4922 °2-0.1603 °2--1.3272 °2
S-0.0149 Å °-0.2502 Å °0.1582 Å °0.0299 Å °-0.0717 Å °0.026 Å °-0.1305 Å °-0.2296 Å °0.0638 Å °
Refinement TLS groupSelection details: all

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