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- PDB-6z03: DNA Topoisomerase -

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Basic information

Entry
Database: PDB / ID: 6z03
TitleDNA Topoisomerase
ComponentsDNA topoisomerase ITopoisomerase
KeywordsDNA BINDING PROTEIN / Topoisomerase
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding
Similarity search - Function
DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain / Topoisomerase I C-terminal domain / DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily / Eukaryotic DNA topoisomerase I, DNA binding fragment / C-terminal topoisomerase domain / DNA Topoisomerase I (eukaryota) ...DNA topoisomerase I, DNA binding, eukaryotic-type / DNA topoisomerase I, DNA binding, N-terminal domain 2 / DNA topoisomerase I, DNA binding, N-terminal domain 1 / DNA topoisomerase I, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha/beta subdomain / Topoisomerase I C-terminal domain / DNA topoisomerase I, DNA binding, eukaryotic-type, N-terminal domain superfamily / Eukaryotic DNA topoisomerase I, DNA binding fragment / C-terminal topoisomerase domain / DNA Topoisomerase I (eukaryota) / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core
Similarity search - Domain/homology
Biological speciesCaldiarchaeum subterraneum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTakahashi, T.S. / Gadelle, D. / Forterre, P. / Mayer, C. / Petrella, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE12-0032 France
CitationJournal: Nat Commun / Year: 2022
Title: Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states.
Authors: Takahashi, D.T. / Gadelle, D. / Agama, K. / Kiselev, E. / Zhang, H. / Yab, E. / Petrella, S. / Forterre, P. / Pommier, Y. / Mayer, C.
History
DepositionMay 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Feb 7, 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 I
B: DNA topoisomerase I


Theoretical massNumber of molelcules
Total (without water)127,1672
Polymers127,1672
Non-polymers00
Water7,800433
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-4 kcal/mol
Surface area53220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.470, 94.680, 92.650
Angle α, β, γ (deg.)90.000, 111.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA topoisomerase I / Topoisomerase


Mass: 63583.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldiarchaeum subterraneum (archaea) / Gene: HGMM_F15C04C08 / Production host: Escherichia coli (E. coli) / References: UniProt: E6NAV3, DNA topoisomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O

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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: 49.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 6000, 1 M LiCl 100mM Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.197→86.016 Å / Num. obs: 61691 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 14.3
Reflection shellResolution: 2.197→2.235 Å / Rmerge(I) obs: 0.982 / Num. unique obs: 3039 / CC1/2: 0.668

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
XDSJan 26, 2018data reduction
autoPROC1.1.7 (20171219)data scaling
MOLREPCCP4Interface 7.0.053phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z01

6z01


Resolution: 2.2→70.07 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.2413 2972 4.82 %
Rwork0.1916 --
obs0.194 61683 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.08 Å2 / Biso mean: 54.8044 Å2 / Biso min: 21.05 Å2
Refinement stepCycle: final / Resolution: 2.2→70.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8707 0 0 433 9140
Biso mean---47.68 -
Num. residues----1043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.230.37941250.282627712896
2.23-2.270.30291530.272427772930
2.27-2.310.32891450.249528002945
2.31-2.360.29391330.242827732906
2.36-2.410.27761310.228527942925
2.41-2.460.31411770.226527362913
2.46-2.510.30031370.2328282965
2.51-2.580.29531400.222527782918
2.58-2.650.29911260.223528002926
2.65-2.730.29851420.231127882930
2.73-2.810.29921470.229328012948
2.81-2.910.26521450.215327552900
2.91-3.030.28621330.230728152948
3.03-3.170.25621270.219528152942
3.17-3.340.26541310.210927862917
3.34-3.540.23451550.187427902945
3.54-3.820.20681300.179228242954
3.82-4.20.21041470.159827992946
4.2-4.810.19381390.153328192958
4.81-6.060.2151620.17127912953
6.06-70.070.20331470.154128713018

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