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

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Basic information

Entry
Database: PDB / ID: 11fc
TitleE.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CTGAACTT
Components
  • DNA (5'-D(P*CP*TP*GP*AP*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
MALONATE ION / DNA / DNA topoisomerase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 CTGAACTT
Authors: Tan, K. / Tse Dinh, Y.C.
History
DepositionFeb 20, 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*CP*TP*GP*AP*AP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8419
Polymers75,3672
Non-polymers4747
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint2 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.794, 133.242, 78.434
Angle α, β, γ (deg.)90.000, 133.984, 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
Components on special symmetry positions
IDModelComponents
11A-923-

HOH

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Components

#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*CP*TP*GP*AP*AP*CP*TP*T)-3')


Mass: 2401.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium Citrate Dibasic, 20% (w/v) PEG 3350 / PH range: 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.1→34.4 Å / Num. obs: 47324 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.058 / Rrim(I) all: 0.109 / Χ2: 0.84 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3478 / CC1/2: 0.884 / Rpim(I) all: 0.507 / Rrim(I) all: 0.922 / Χ2: 0.69 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.31 Å / SU ML: 0.2446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 2303 4.9 %
Rwork0.2272 44718 -
obs0.2291 47021 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 162 31 135 5252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255241
X-RAY DIFFRACTIONf_angle_d0.50327129
X-RAY DIFFRACTIONf_chiral_restr0.0409790
X-RAY DIFFRACTIONf_plane_restr0.0068910
X-RAY DIFFRACTIONf_dihedral_angle_d17.8512002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.38421400.35842577X-RAY DIFFRACTION91.98
2.14-2.190.37141560.33442790X-RAY DIFFRACTION99.09
2.19-2.250.35821430.31912770X-RAY DIFFRACTION98.61
2.25-2.310.36081850.30732743X-RAY DIFFRACTION98.69
2.31-2.370.33711330.29332796X-RAY DIFFRACTION99.15
2.37-2.450.30831380.28812790X-RAY DIFFRACTION98.69
2.45-2.540.34421450.2962814X-RAY DIFFRACTION99.16
2.54-2.640.32271190.29152799X-RAY DIFFRACTION99.18
2.64-2.760.37421500.28572788X-RAY DIFFRACTION99.49
2.76-2.910.28321570.27472812X-RAY DIFFRACTION99.46
2.91-3.090.30991490.27082809X-RAY DIFFRACTION99.66
3.09-3.330.2821320.26152832X-RAY DIFFRACTION99.76
3.33-3.660.27051540.21982799X-RAY DIFFRACTION99.83
3.66-4.190.19891540.19022834X-RAY DIFFRACTION99.97
4.19-5.270.20181280.16592858X-RAY DIFFRACTION100
5.27-34.310.20621200.17152907X-RAY DIFFRACTION99.9
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)
11.71209311188-1.095236323580.04687253519496.816767238981.982157237651.955295088510.145394828758-0.436157999399-0.176555893097-0.02630727973880.063152045899-0.09527620969080.102299717491-0.407244294297-0.2102376407120.375410715997-0.182632533826-0.04023025961410.5892828042890.1485692428620.301675776917-24.0740306179-21.43955889338.82608094148
21.58790525132-0.265676463685-0.2541993311421.314170230550.3216969433511.469382629540.08640750799790.02615144953160.363925758816-0.27183463510.00285218791365-0.223952445453-0.27582945087-0.0419397482374-0.09148629487780.3363680332080.004642573855780.02298072089760.288405526419-0.002350766087570.295860876866-10.50917479598.92503538503-11.690553398
31.612981695190.0744718125808-0.4063551714931.187338002060.3841754024840.709823922559-0.166799082151-0.665679291090.3013414717020.3451026650290.07248409969990.159416586073-0.400405580934-0.364623543123-0.0002975900716160.3766629872120.108121470668-0.01318673322360.633493091016-0.1215465992190.32779983215-24.62589906869.3462392776213.9628506165
42.98533221433-2.70973316828-2.895450983399.028727400871.04002059283.19491845207-0.004627103749980.0321626076624-0.4403305997-0.394455133158-0.3418916149210.8449599868240.379859613795-1.285572435760.2978925413970.435034279124-0.0632424815047-0.03410870294980.81829577076-0.05587571439180.354462930642-30.0799735689-5.14865803884.68999352107
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 )BI701 - 708

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