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

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Basic information

Entry
Database: PDB / ID: 11lb
TitleE.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo GCAACTGG
Components
  • DNA (5'-D(P*AP*AP*CP*TP*GP*G)-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 / 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
ACETATE ION / CITRATE ANION / DNA / DNA topoisomerase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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: Sci Rep / Year: 2026
Title: New Insights into Binding of G-segment DNA to the Active Site of Escherichia coli Topoisomerase III.
Authors: Tan, K. / Annamalai, T. / Stols, L. / Bhuiyan, M.A.R. / Tse-Dinh, Y.C.
History
DepositionMar 2, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: 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.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 3
B: DNA (5'-D(P*AP*AP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,54915
Polymers75,4172
Non-polymers1,13213
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-20 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.685, 120.884, 85.609
Angle α, β, γ (deg.)90.000, 99.344, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,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: 72965.398 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*AP*CP*TP*GP*G)-3')


Mass: 2451.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 368 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Citrate, 20%(w/V)PEG 4000, 10% (v/v) 2-Propanol

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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: Nov 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→60.5 Å / Num. obs: 64910 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.051 / Rrim(I) all: 0.11 / Χ2: 0.9 / Net I/σ(I): 8.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4763 / CC1/2: 0.454 / Rpim(I) all: 0.481 / Rrim(I) all: 1.04 / Χ2: 88 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→60.44 Å / SU ML: 0.2228 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3356
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2118 3178 4.92 %
Rwork0.1778 61403 -
obs0.1795 64581 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.75 Å2
Refinement stepCycle: LAST / Resolution: 1.85→60.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 125 78 355 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01275283
X-RAY DIFFRACTIONf_angle_d1.14087176
X-RAY DIFFRACTIONf_chiral_restr0.0725786
X-RAY DIFFRACTIONf_plane_restr0.0114921
X-RAY DIFFRACTIONf_dihedral_angle_d18.20442025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.38171380.31532557X-RAY DIFFRACTION95.98
1.88-1.910.3031380.26652668X-RAY DIFFRACTION97.26
1.91-1.940.24921150.23472688X-RAY DIFFRACTION97.43
1.94-1.970.26921250.22932638X-RAY DIFFRACTION97.25
1.97-2.010.29481420.21792663X-RAY DIFFRACTION97.94
2.01-2.050.20381300.21192704X-RAY DIFFRACTION97.42
2.05-2.090.25731310.20632629X-RAY DIFFRACTION97.46
2.09-2.130.26621450.20482530X-RAY DIFFRACTION92.95
2.13-2.180.26451260.20292560X-RAY DIFFRACTION94.71
2.18-2.240.22411390.19832688X-RAY DIFFRACTION98.26
2.24-2.30.24991450.19172697X-RAY DIFFRACTION98.61
2.3-2.370.2141350.17712676X-RAY DIFFRACTION98.84
2.37-2.440.23391570.18342714X-RAY DIFFRACTION98.8
2.44-2.530.2311400.18132665X-RAY DIFFRACTION98.8
2.53-2.630.22051100.17552739X-RAY DIFFRACTION98.92
2.63-2.750.20321330.18182747X-RAY DIFFRACTION99.14
2.75-2.90.21161390.18532656X-RAY DIFFRACTION98.73
2.9-3.080.22081610.1862576X-RAY DIFFRACTION95.2
3.08-3.310.20181260.16542702X-RAY DIFFRACTION98.43
3.31-3.650.18721550.16022738X-RAY DIFFRACTION99.79
3.65-4.180.18561560.14342713X-RAY DIFFRACTION99.69
4.18-5.260.16191630.14632724X-RAY DIFFRACTION99.48
5.26-60.440.20181290.17162731X-RAY DIFFRACTION97.48
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)
13.3465832997-0.94762099609-0.9200268742393.01718096601-0.8235280843662.712486828450.04495896634520.49764733555-0.20818814-0.627367482681-0.0684302346525-0.4366561315380.2852313466690.514199141299-0.02919697739280.2760316328790.03645621952380.0588570456020.34010570594-0.02833995799720.23895772454915.3606085266-10.675503466-15.3735912141
20.161683996165-0.643349201703-0.2786821457742.589779087771.265103643610.652898701363-0.03433361074130.09274560669360.0520640442885-0.3251889893680.105555392246-0.285976376993-0.08078871226640.0831709867511-0.1066850856650.296934256192-0.0438840069910.04810522037980.2525986859140.02513547784890.27466361449611.444219165116.6584044129-8.0344198425
31.1445145135-0.1158149013320.2359751139861.43120523581-0.3222835668362.56404617308-0.0315045218010.179564876104-0.0427092939519-0.2861539370070.07349084406720.1408633688070.0423132656748-0.2304280206330.04621531791550.294563477596-0.02060775227620.0258817417270.243008006521-0.009905008434770.2012410388612.45282615973-5.75942787549-12.2300271781
40.6923520965330.330369526064-0.6304851973910.801343065501-0.9712241767721.546449662990.0158901560111-0.1406789332110.04282163640870.147635415979-0.02011700870630.0442430289236-0.0967854207158-0.00396476526118-0.02013731127670.2119663649010.00275485639867-0.006034122993730.161076100618-0.009054178913950.176538803784-3.0925684932610.085372815524.2414714344
50.26878825387-0.131513662333-0.3822991017990.7011367605550.3960429905251.70598877683-0.0361822167471-0.0148018937248-0.1156788648850.0822606897957-0.0554857556302-0.01836228061610.0587246701367-0.1891127218720.05618558503720.1032795982090.00248068428255-0.02265425208860.1449236908310.0166890732080.15949081346-3.43875671511-13.607771368821.0705796354
60.207447187624-0.402419198899-0.5584005481540.671511843330.9460971821911.30875973901-0.108970248634-0.111331121324-0.07998997311910.2204641694890.03847366702470.1205101689590.173244838784-0.1307499619480.06544061321850.384298605054-0.01730302493910.05435373868290.408296173480.05251720407790.21846772653-13.4354531668-15.513691538340.3591590776
71.290461475220.205200873822-0.5574333922362.55479794097-0.3177406869211.65739129882-0.0375207679954-0.00114710354007-0.03270920230950.1372151322380.03867174210510.27327943537-0.0540598126688-0.214793895797-0.001015674114450.1248835350050.01359396752510.005525250278490.1277154493420.01578719174610.168121001838-1.858439327149.5755552647515.8680138894
81.86011648235-0.447138688253-0.8173612242913.62284251429-0.1970674682792.086922572420.174496329745-0.08420827442510.06478371806390.4549493742180.103352794534-0.046657166907-0.364960480835-0.111502844862-0.2743176529520.3119568381290.05576021717760.03026112374480.2341095439680.01786672455370.2519427913770.040931812075527.03463390189.23848414183
93.61319390162-0.481310989650.1682476112655.930502599291.238442615567.36778151625-0.270958387830.2072578158140.0508275491386-0.6110374627870.124940451701-1.14199304887-0.4303291506590.8972366202020.1386255206920.239650199707-0.02137623121370.02425951632760.2628135364110.06043498258150.32535796087311.382994840616.82476060354.83329468643
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 40 )AA1 - 401 - 40
22chain 'A' and (resid 41 through 92 )AA41 - 9241 - 92
33chain 'A' and (resid 93 through 158 )AA93 - 15893 - 158
44chain 'A' and (resid 159 through 241 )AA159 - 241159 - 241
55chain 'A' and (resid 242 through 429 )AA242 - 429242 - 429
66chain 'A' and (resid 430 through 484 )AA430 - 484430 - 484
77chain 'A' and (resid 485 through 587 )AA485 - 587485 - 587
88chain 'A' and (resid 588 through 620 )AA588 - 620588 - 620
99chain 'B' and (resid 710 through 715 )BO710 - 715

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