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Entry
Database: PDB / ID: 8qmb
TitleNucleant-assisted 2.0 A resolution structure of the Streptococcus pneumoniae topoisomerase IV-V18mer DNA complex with the novel fluoroquinolone Delafloxacin
Components
  • DNA (5'-D(GP*TP*AP*AP*TP*AP*C)-3')
  • DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3')
  • DNA (5'-D(TP*GP*TP*GP*GP*AP*T)-3')
  • DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
KeywordsISOMERASE / PROTEIN-DNA CLEAVAGE COMPLEX / TOPOISOMERASE IIA / DELAFLOXACIN / TOPOISOMERASE IV-DNA-ANTIBIOTIC COMPLEX / PEGylated GRAPHENE
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / extrinsic component of plasma membrane / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / MALONIC ACID / delafloxacin / DNA / DNA (> 10) / DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: To Be Published
Title: The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin.
Authors: Najmudin, S. / Pan, X.S. / Wang, B. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R.
History
DepositionSep 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: 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 4 subunit B,DNA topoisomerase 4 subunit A
B: DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A
E: DNA (5'-D(TP*GP*TP*GP*GP*AP*T)-3')
F: DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3')
G: DNA (5'-D(GP*TP*AP*AP*TP*AP*C)-3')
H: DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,44429
Polymers179,3636
Non-polymers2,08123
Water19,0781059
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19730 Å2
ΔGint-164 kcal/mol
Surface area61580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.215, 157.215, 211.948
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 411 - 1486 / Label seq-ID: 9 - 732

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit A / Topoisomerase IV subunit B / 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: The 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 ...Details: The 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),The 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),The 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),The 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: parE, SP_0852, parC, SP_0855 / Plasmid: PET29A / Production host: Escherichia coli (E. coli)
References: UniProt: Q59961, UniProt: P72525, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 4 types, 4 molecules EFGH

#2: DNA chain DNA (5'-D(TP*GP*TP*GP*GP*AP*T)-3')


Mass: 2168.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: plamid pBR322 / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*A)-3')


Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: plasmid pBR322 / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(GP*TP*AP*AP*TP*AP*C)-3')


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: plasmid pBR322 / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (5'-D(P*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*C)-3')


Mass: 3317.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: plasmid pBR322 / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 8 types, 1082 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


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


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


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: 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
#10: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1059 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.22 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 5.5-7.0% Isopropanol, 0.05 mg/mL PEGylated graphene as a nucleant. 30% MPD as cryoprotectant and 1 mM beta-mercaptoethanol in the mother liquor.
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.997→83.768 Å / Num. obs: 115609 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 100.1 % / CC1/2: 1 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.024 / Rrim(I) all: 0.24 / Net I/σ(I): 19
Reflection shellResolution: 1.997→2.306 Å / Redundancy: 82.3 % / Rmerge(I) obs: 2.948 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6766 / CC1/2: 0.827 / Rpim(I) all: 0.326 / Rrim(I) all: 2.966 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
xia2data scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→83.628 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.887 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.178
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2064 5806 5.022 %
Rwork0.1687 109796 -
all0.171 --
obs-115602 56.762 %
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: 47.121 Å2
Baniso -1Baniso -2Baniso -3
1--0.007 Å2-0.004 Å20 Å2
2---0.007 Å2-0 Å2
3---0.023 Å2
Refinement stepCycle: LAST / Resolution: 2→83.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11512 732 134 1059 13437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01212690
X-RAY DIFFRACTIONr_bond_other_d0.0030.01611960
X-RAY DIFFRACTIONr_angle_refined_deg2.261.85217258
X-RAY DIFFRACTIONr_angle_other_deg0.8641.7827584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08251456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12592
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg3.953525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.625102229
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.88410551
X-RAY DIFFRACTIONr_chiral_restr0.1170.21922
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214339
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022749
X-RAY DIFFRACTIONr_nbd_refined0.2080.22715
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1580.211417
X-RAY DIFFRACTIONr_nbtor_refined0.1740.26103
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.27217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2957
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.25
X-RAY DIFFRACTIONr_metal_ion_refined0.040.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.221
X-RAY DIFFRACTIONr_nbd_other0.1360.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2260.217
X-RAY DIFFRACTIONr_mcbond_it4.3813.6065810
X-RAY DIFFRACTIONr_mcbond_other4.3823.6065811
X-RAY DIFFRACTIONr_mcangle_it6.5326.4737259
X-RAY DIFFRACTIONr_mcangle_other6.5326.4747260
X-RAY DIFFRACTIONr_scbond_it5.724.1366880
X-RAY DIFFRACTIONr_scbond_other5.724.1366880
X-RAY DIFFRACTIONr_scangle_it8.3747.3819992
X-RAY DIFFRACTIONr_scangle_other8.3747.3819993
X-RAY DIFFRACTIONr_lrange_it10.30237.1515126
X-RAY DIFFRACTIONr_lrange_other10.30137.15115124
X-RAY DIFFRACTIONr_ncsr_local_group_10.10.0523368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.100270.05008
12AX-RAY DIFFRACTIONLocal ncs0.100270.05008
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
2-2.0520.402200.281920.29148880.8770.9351.4240.28
2.052-2.1080.352530.2397210.246145740.9290.9615.31080.23
2.108-2.1690.297700.23812600.241141600.9480.9639.39270.222
2.169-2.2360.279940.23418520.236137800.9430.96314.12190.214
2.236-2.3090.2861260.2224950.223133830.9460.96919.58450.197
2.309-2.390.2512010.22135740.223128480.9580.96929.3820.191
2.39-2.480.272310.22348050.225124960.9550.9740.30090.192
2.48-2.5810.33440.23362670.236120600.9430.96654.81760.202
2.581-2.6960.2534570.22789880.228115020.9550.96782.11610.191
2.696-2.8280.2695500.221104810.223110500.9540.96999.8280.186
2.828-2.980.2394520.19100250.192104890.9650.97899.88560.161
2.98-3.1610.2234920.18294700.18499760.9670.9899.85970.16
3.161-3.3790.2154850.17688870.17893770.9730.98399.94670.162
3.379-3.6490.2164420.17283200.17487630.9740.98599.98860.161
3.649-3.9970.1853960.14776550.14980510.980.9881000.139
3.997-4.4670.173770.1369320.13273100.9830.9999.98630.125
4.467-5.1560.1633760.12161130.12364890.9840.9921000.119
5.156-6.3080.1822770.1552690.15155460.9820.991000.148
6.308-8.8960.1832190.14141070.14343260.9830.9891000.143
8.896-83.6280.1721440.18323850.18225310.9850.93899.9210.214
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)
10.69510.2653-0.05510.32740.00430.3636-0.0176-0.0061-0.1104-0.00360.0153-0.09660.06670.09320.00230.01230.01690.0020.0245-0.00340.0307-47.514259.377-36.3811
20.64590.31290.00430.32640.01440.18310.0229-0.05250.1193-0.0188-0.01840.0265-0.09450.0136-0.00450.0553-0.00510.01250.0133-0.00930.0281-53.302267.10770.0597
Refinement TLS groupSelection: ALL

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