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Basic information

Entry
Database: PDB / ID: 8qmc
TitleHigh resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and novel fluoroquinolone Delafloxacin
Components
  • DNA (5'-D(*T)-R(P*G)-D(P*T)-R(P*GP*GP*A)-D(P*T)-3')
  • DNA topoisomerase (ATP-hydrolyzing),DNA topoisomerase 4 subunit A
  • DNA/RNA (5'-R(*G)-D(P*T)-R(P*AP*A)-D(P*T)-R(P*AP*C)-3')
  • DNA/RNA (5'-R(P*AP*AP*CP*CP*G)-D(P*T)-R(P*A)-D(P*TP*T)-R(P*AP*C)-3')
  • DNA/RNA (5'-R(P*GP*G)-D(P*TP*T)-R(P*A)-D(P*T)-R(P*CP*CP*AP*CP*A)-3')
KeywordsISOMERASE / PROTEIN-DNA CLEAVAGE COMPLEX / TOPOISOMERASE IIA / DELAFLOXACIN / TOPOISOMERASE IV-DNA-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / cytoplasm
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A ...DNA topoisomerase IV subunit A, Gram-positive / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / MALONIC ACID / delafloxacin / DNA / DNA (> 10) / : / DNA topoisomerase 4 subunit A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsNajmudin, S. / Pan, X.S. / Wang, B. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T000848/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of topoisomerase targeting by delafloxacin.
Authors: Najmudin, S. / Pan, X.S. / Wang, B. / Govada, L. / Chayen, N.E. / Rubio, N. / Shaffer, M.S.P. / Rzepa, H.S. / Fisher, L.M. / Sanderson, M.R.
History
DepositionSep 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase (ATP-hydrolyzing),DNA topoisomerase 4 subunit A
B: DNA topoisomerase (ATP-hydrolyzing),DNA topoisomerase 4 subunit A
E: DNA (5'-D(*T)-R(P*G)-D(P*T)-R(P*GP*GP*A)-D(P*T)-3')
F: DNA/RNA (5'-R(P*GP*G)-D(P*TP*T)-R(P*A)-D(P*T)-R(P*CP*CP*AP*CP*A)-3')
H: DNA/RNA (5'-R(P*AP*AP*CP*CP*G)-D(P*T)-R(P*A)-D(P*TP*T)-R(P*AP*C)-3')
G: DNA/RNA (5'-R(*G)-D(P*T)-R(P*AP*A)-D(P*T)-R(P*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,90621
Polymers179,3636
Non-polymers1,54315
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.140, 157.140, 211.636
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1751-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA topoisomerase (ATP-hydrolyzing),DNA topoisomerase 4 subunit A / Topoisomerase IV subunit A


Mass: 84211.422 Da / Num. of mol.: 2 / Mutation: Insertion of His at postion 648
Source method: isolated from a genetically manipulated source
Details: he fused TOPOISOMERASE IV CLEAVAGE COMPLEX comprises the C-terminal domain of the ParE30 domain (residues 415-647), a His insert at position 648 and the N-terminal domain of ParC55 (residues ...Details: he fused TOPOISOMERASE IV CLEAVAGE COMPLEX comprises the C-terminal domain of the ParE30 domain (residues 415-647), a His insert at position 648 and the N-terminal domain of ParC55 (residues 1001-1486),he fused TOPOISOMERASE IV CLEAVAGE COMPLEX comprises the C-terminal domain of the ParE30 domain (residues 415-647), a His insert at position 648 and the N-terminal domain of ParC55 (residues 1001-1486)
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: 7785 / Gene: AMCSP13_000989, parC, SP_0855 / Plasmid: pET29A / Production host: Escherichia coli (E. coli)
References: UniProt: J0V1V8, UniProt: P72525, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 4 types, 4 molecules EFHG

#2: DNA chain DNA (5'-D(*T)-R(P*G)-D(P*T)-R(P*GP*GP*A)-D(P*T)-3')


Mass: 2168.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: pBR322 / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA/RNA (5'-R(P*GP*G)-D(P*TP*T)-R(P*A)-D(P*T)-R(P*CP*CP*AP*CP*A)-3')


Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: pBR322 / Source: (synth.) DNA molecule (others)
#4: DNA chain DNA/RNA (5'-R(P*AP*AP*CP*CP*G)-D(P*T)-R(P*A)-D(P*TP*T)-R(P*AP*C)-3')


Mass: 3317.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: pBR322 / Source: (synth.) DNA molecule (others)
#5: DNA chain DNA/RNA (5'-R(*G)-D(P*T)-R(P*AP*A)-D(P*T)-R(P*AP*C)-3')


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: pBR322 / Source: (synth.) DNA molecule (others)

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Non-polymers , 7 types, 441 molecules

#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#11: Chemical ChemComp-TE9 / delafloxacin / 1-[6-azanyl-3,5-bis(fluoranyl)pyridin-2-yl]-8-chloranyl-6-fluoranyl-7-(3-oxidanylazetidin-1-yl)-4-oxidanylidene-quinoline-3-carboxylic acid


Mass: 440.760 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H12ClF3N4O4 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.21 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop
Details: 2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 5.5-7.0% Isopropanol. 30% MPD as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.402→64.862 Å / Num. obs: 60189 / % possible obs: 96.2 % / Redundancy: 20.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.078 / Rrim(I) all: 0.349 / Net I/σ(I): 10.3
Reflection shellResolution: 2.402→2.891 Å / Redundancy: 20.8 % / Rmerge(I) obs: 2.05 / Mean I/σ(I) obs: 2 / Num. unique obs: 5142 / CC1/2: 0.745 / Rpim(I) all: 0.459 / Rrim(I) all: 2.102 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB-REDOrefinement
DIALSdata scaling
xia2data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→64.862 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.814 / SU B: 23.757 / SU ML: 0.265 / Cross valid method: FREE R-VALUE / ESU R: 1.101 / ESU R Free: 0.434
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2992 3063 5.104 %
Rwork0.2413 56954 -
all0.244 --
obs-60017 50.895 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.352 Å2
Baniso -1Baniso -2Baniso -3
1--0.546 Å2-0.273 Å2-0 Å2
2---0.546 Å2-0 Å2
3---1.772 Å2
Refinement stepCycle: LAST / Resolution: 2.402→64.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11512 732 98 426 12768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01212642
X-RAY DIFFRACTIONr_bond_other_d0.0030.01611549
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.66317213
X-RAY DIFFRACTIONr_angle_other_deg0.4491.56426964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.14751454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.664592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89102227
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.53410550
X-RAY DIFFRACTIONr_chiral_restr0.0680.21917
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022331
X-RAY DIFFRACTIONr_nbd_refined0.2380.22998
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.211834
X-RAY DIFFRACTIONr_nbtor_refined0.1830.26029
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.26719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2438
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.22
X-RAY DIFFRACTIONr_metal_ion_refined0.010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2380.219
X-RAY DIFFRACTIONr_nbd_other0.2240.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.210
X-RAY DIFFRACTIONr_mcbond_it0.7051.2055803
X-RAY DIFFRACTIONr_mcbond_other0.7041.2055803
X-RAY DIFFRACTIONr_mcangle_it1.191.8027251
X-RAY DIFFRACTIONr_mcangle_other1.191.8037252
X-RAY DIFFRACTIONr_scbond_it0.5351.2096839
X-RAY DIFFRACTIONr_scbond_other0.5351.2086840
X-RAY DIFFRACTIONr_scangle_it0.9281.7879955
X-RAY DIFFRACTIONr_scangle_other0.9281.7869956
X-RAY DIFFRACTIONr_lrange_it2.35613.96714858
X-RAY DIFFRACTIONr_lrange_other2.35313.96514846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.402-2.4650.57670.4021130.41686570.7790.8541.38620.387
2.465-2.5320.4290.3832810.38484110.9350.8613.44790.38
2.532-2.6050.422300.3645300.36781390.8460.9126.88050.332
2.605-2.6850.407410.3498050.35279720.8790.92110.61210.326
2.685-2.7730.347540.31410670.31677150.9120.93314.53010.281
2.773-2.870.407780.32716040.33174450.9040.9322.59230.292
2.87-2.9780.3911010.30621230.30972100.9060.93930.8460.273
2.978-3.10.391190.29125260.29669500.9140.94538.05760.255
3.1-3.2370.3161830.29335260.29466810.9340.94355.51560.252
3.237-3.3950.3232440.29646130.29763690.9290.94676.260.255
3.395-3.5780.3953060.31856110.32260950.8830.93697.07960.268
3.578-3.7940.3482950.28554000.28857670.9190.94898.75150.243
3.794-4.0550.3222690.25750640.2654350.9320.95898.12330.225
4.055-4.3790.2582600.19947960.20250620.9620.97599.88150.179
4.379-4.7950.2312720.17744010.1846770.9690.98199.91450.165
4.795-5.3570.2642270.18340170.18742470.9630.98199.92940.17
5.357-6.1790.2771880.20135790.20537690.9610.97799.94690.191
6.179-7.550.2711710.18430610.18932320.9590.981000.18
7.55-10.6060.1711480.14923910.1525410.9840.98699.92130.152
10.606-64.8620.26610.20914460.21215070.970.9641000.232
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)
10.9570.3499-0.09510.5253-0.01170.4778-0.004-0.0306-0.17860.03940.002-0.2020.07620.20850.00190.0590.02450.00270.0931-0.00590.0874-46.958159.5613-36.2153
20.92920.5303-0.01440.5027-0.00560.30130.0172-0.00110.2246-0.0341-0.00290.0636-0.17460.0417-0.01420.12470.00120.02230.0476-0.0040.0758-53.048767.7406-0.1185
34.2438-2.47740.37337.1638-4.02132.5827-0.1221-0.27570.69380.2590.0125-0.4769-0.16740.12920.10960.1032-0.0545-0.02820.1889-0.05030.1155-36.689669.2553-35.6808
41.28950.6182-0.15580.39620.65715.75370.06440.02160.44-0.0756-0.00120.1828-0.86550.1319-0.06320.17070.0369-0.00890.2160.07680.2803-32.839470.5205-31.2398
51.60.9165-0.72960.6814-0.24030.5489-0.0393-0.305-0.38890.09360.0685-0.43530.16170.4592-0.02910.43460.0943-0.18260.6385-0.13660.4365-36.973275.9153-4.0232
66.2422-2.44313.57846.5008-0.98172.0963-0.14680.23080.2979-0.10420.0328-0.896-0.11950.1770.1140.1098-0.05250.02910.10990.00260.1282-39.666372.5461-0.0678
Refinement TLS groupSelection: ALL

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