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- PDB-11yy: E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo AC... -

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Basic information

Entry
Database: PDB / ID: 11yy
TitleE.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo ACTGACTT
Components
  • DNA (5'-D(P*AP*CP*TP*GP*AP*CP*TP*T)-3')
  • DNA topoisomerase 3
KeywordsISOMERASE/DNA / EcTopo3 / ssDNA complex / ISOMERASE / ISOMERASE-DNA complex
Function / homology
Function and homology information


cytoplasmic replication fork / sequence-specific single stranded DNA binding / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA-templated DNA replication / DNA recombination / DNA repair / magnesium ion binding
Similarity search - Function
DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central ...DNA topoisomerase III / DNA topoisomerase 3-like, TOPRIM domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain
Similarity search - Domain/homology
MALONIC ACID / SUCCINIC ACID / DNA / DNA topoisomerase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTan, K. / Tse Dinh, Y.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139817 United States
CitationJournal: To Be Published
Title: E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo ACTGACTT
Authors: Tan, K. / Tse Dinh, Y.C.
History
DepositionMar 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: 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 3
B: DNA (5'-D(P*AP*CP*TP*GP*AP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0789
Polymers74,5722
Non-polymers5067
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-11 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.912, 132.372, 78.777
Angle α, β, γ (deg.)90.000, 134.236, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein DNA topoisomerase 3 / DNA topoisomerase III


Mass: 72170.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: topB, b1763, JW1752 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: P14294, DNA topoisomerase
#2: DNA chain DNA (5'-D(P*AP*CP*TP*GP*AP*CP*TP*T)-3')


Mass: 2401.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 115 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2M Ammonium Citrate Dibasic, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→56.44 Å / Num. obs: 40486 / % possible obs: 99.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.03 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.043 / Rrim(I) all: 0.103 / Χ2: 0.83 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3006 / CC1/2: 0.67 / Rpim(I) all: 0.478 / Rrim(I) all: 1.16 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→56.44 Å / SU ML: 0.3536 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8864
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 2002 4.97 %
Rwork0.2166 38290 -
obs0.2176 40292 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→56.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4911 162 32 108 5213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00265222
X-RAY DIFFRACTIONf_angle_d0.56297106
X-RAY DIFFRACTIONf_chiral_restr0.0412789
X-RAY DIFFRACTIONf_plane_restr0.0057909
X-RAY DIFFRACTIONf_dihedral_angle_d17.57711990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.38511440.3532708X-RAY DIFFRACTION97.6
2.26-2.320.37521390.34632699X-RAY DIFFRACTION97.76
2.32-2.380.34111500.32722691X-RAY DIFFRACTION97.36
2.38-2.460.30131350.30132689X-RAY DIFFRACTION96.25
2.46-2.550.30131330.29922662X-RAY DIFFRACTION96.55
2.55-2.650.32251400.29232723X-RAY DIFFRACTION99.51
2.65-2.770.29411460.29082774X-RAY DIFFRACTION99.73
2.77-2.920.33911360.28112791X-RAY DIFFRACTION99.63
2.92-3.10.32371520.26812704X-RAY DIFFRACTION99.48
3.1-3.340.2751470.24212787X-RAY DIFFRACTION99.56
3.34-3.680.22371380.21632715X-RAY DIFFRACTION97.71
3.68-4.210.19811470.17472766X-RAY DIFFRACTION100
4.21-5.30.16391420.1562800X-RAY DIFFRACTION99.83
5.3-56.440.17311530.16092781X-RAY DIFFRACTION98.52
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.15646166486-2.09070594996-0.6299035125448.472923794992.814613629122.206291528850.461814437719-0.493041395541-0.397944623165-0.194984292082-0.203915672546-0.388398229654-0.0605627918290.0116835973534-0.2504865989630.4830951929-0.218364960761-0.05563023129230.4844968159110.1475040665420.4634572959383.61200514437-21.991661967837.1859991436
22.71818991740.08001479436040.3087484490741.365825255730.02505008512111.315698413320.150879620710.4790810787650.54650259266-0.205389850635-0.15704386884-0.120554674659-0.09475850133510.101293165122-0.006675492425410.3551984997730.009737584477020.03204581977560.3958357610210.07022531545110.39019638705816.81409694458.1671109377816.5715052778
33.01058016361-0.8984690331720.5022903922222.41766970909-0.7438871282892.516097945220.0400244714474-0.7987519637220.5996345345370.326603037086-0.08913367363150.171627465318-0.330176557564-0.2890688392710.03182934923780.391111469807-0.1200148742110.07507622206930.55071819158-0.2039186661080.4801476873122.76015389458.5664917216542.2178288216
46.055559986462.194679604921.58357755376.96254553494-0.5003287166395.879866325470.4365646751141.10936638849-1.04138971385-0.897540158037-0.7072912387821.064750524051.20898274457-1.040945839270.3541347237090.743137865817-0.190953726317-0.01985191144760.734313674065-0.2262148541810.53437929084-2.7895150565-5.6799174734932.6038304027
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 151 )AA1 - 1511 - 151
22chain 'A' and (resid 152 through 546 )AA152 - 546152 - 546
33chain 'A' and (resid 547 through 620 )AA547 - 620547 - 620
44chain 'B' and (resid 701 through 708 )BG701 - 708

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