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- PDB-6z01: DNA Topoisomerase -

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Basic information

Entry
Database: PDB / ID: 6z01
TitleDNA Topoisomerase
ComponentsDNA topoisomerase I
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 / SAD / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase I
B: DNA topoisomerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62414
Polymers128,1982
Non-polymers42512
Water20,1951121
1
A: DNA topoisomerase I
hetero molecules

B: DNA topoisomerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,62414
Polymers128,1982
Non-polymers42512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area4480 Å2
ΔGint-141 kcal/mol
Surface area53860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.200, 96.590, 94.560
Angle α, β, γ (deg.)90.000, 113.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA topoisomerase I


Mass: 64099.105 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: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97903 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.9→35.44 Å / Num. obs: 98987 / % possible obs: 99.82 % / Redundancy: 9.85 % / CC1/2: 0.983 / CC star: 0.996 / Net I/σ(I): 16.17
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 9850 / CC1/2: 0.687 / CC star: 0.902 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.44 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 4941 5 %
Rwork0.1798 93885 -
obs0.1816 98826 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.78 Å2 / Biso mean: 42.8161 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 1.9→35.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8659 0 12 1121 9792
Biso mean--44.97 43.32 -
Num. residues----1038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.3251650.267731303295100
1.92-1.940.35691630.276530833246100
1.94-1.970.30261650.249331403305100
1.97-1.990.29291630.230431013264100
1.99-2.020.25591660.21631473313100
2.02-2.050.2821640.211231173281100
2.05-2.080.23451630.203331053268100
2.08-2.110.27441660.202531413307100
2.11-2.140.23151630.200131063269100
2.14-2.170.22081650.188731353300100
2.17-2.210.231640.18831153279100
2.21-2.250.26951660.200731623328100
2.25-2.30.27541640.190930983262100
2.3-2.340.25721640.19731173281100
2.34-2.390.22211630.184331093272100
2.39-2.450.23471660.18831463312100
2.45-2.510.25791650.188531463311100
2.51-2.580.22091630.192830993262100
2.58-2.650.25061660.183231503316100
2.65-2.740.25461640.188431093273100
2.74-2.840.21321660.185231573323100
2.84-2.950.23281650.190831263291100
2.95-3.090.24431640.19131193283100
3.09-3.250.22011650.182231433308100
3.25-3.450.19451650.17431333298100
3.45-3.720.20131650.16613128329399
3.72-4.090.18421640.15563141330599
4.09-4.680.1721660.15023145331199
4.68-5.890.19561650.16313142330799
5.9-35.440.17361680.16813195336399
Refinement TLS params.Method: refined / Origin x: -5.1116 Å / Origin y: 69.5764 Å / Origin z: -18.9399 Å
111213212223313233
T0.1443 Å2-0.0167 Å2-0.0014 Å2-0.1357 Å20.0064 Å2--0.1324 Å2
L0.1675 °2-0.1022 °20.0088 °2-0.1087 °20.013 °2--0.0175 °2
S0.0171 Å °-0.0043 Å °-0.0385 Å °-0.0397 Å °-0.009 Å °0.0319 Å °-0.0048 Å °0.0042 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 523
2X-RAY DIFFRACTION1allB4 - 524
3X-RAY DIFFRACTION1allC1 - 13
4X-RAY DIFFRACTION1allS1 - 1121

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