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Basic information

Entry
Database: PDB / ID: 9gef
TitleExperimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex
Components
  • DNA (5'-D(*GP*TP*AP*AP*TP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*GP*GP*AP*T)-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 TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4
KeywordsDNA BINDING PROTEIN / metal ions / Type II topoisomerases / Fluoroquinolones / Long-wavelength X-ray crystallography
Function / homologyACETATE ION / : / delafloxacin / DNA / DNA (> 10)
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsWang, B. / Najmudin, S. / Pan, X.-S. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Govada, L. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other governmentMR/T000848 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases.
Authors: Wang, B. / Najmudin, S. / Pan, X.S. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Govada, L. / Chayen, N.E. / Fisher, L.M. / Sanderson, M.R.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2026Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list

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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
B: DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4
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)176,70427
Polymers174,8106
Non-polymers1,89421
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-171 kcal/mol
Surface area61690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.533, 158.533, 210.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4


Mass: 81934.758 Da / Num. of mol.: 2
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 (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: 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: PLAMID 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: PLAMID PBR322 / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 7 types, 129 molecules

#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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 / Comment: antibiotic*YM
#12: 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: 4.37 Å3/Da / Density % sol: 71.88 % / Description: rod-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were cryoprotected with 50 mM sodium cacodylate pH ...Details: 50 mM sodium cacodylate, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 5.5-7% isopropanol, pH 6.5. The protein crystals were cryoprotected with 50 mM sodium cacodylate pH 6.5, 62.5 mM KCl, 7.5 mM MgCl 2 , 2.5% Tacsimate TM Hampton Research, 1 mM beta-mercaptoethanol and 30% v/v MPD before being flash-cooled in liquid nitrogen and collected in elliptical polyimide sample mounts.
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: I23 / Wavelength: 2.75,3.14,3.54,4.35,4.50,5.16
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
12.751
23.141
33.541
44.351
54.51
65.161
ReflectionResolution: 2.37→210.82 Å / Num. obs: 124385 / % possible obs: 100 % / Redundancy: 59.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.027 / Net I/σ(I): 11.6
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 45 % / Rmerge(I) obs: 5.369 / Num. unique obs: 6112 / CC1/2: 0.204 / Rpim(I) all: 0.796 / % possible all: 100

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Processing

Software
NameVersionClassification
PDB-REDO8.11refinement
PHENIX4.4.7refinement
DIALSdata reduction
xia2.multiplexdata scaling
DIMPLEphasing
STARANISOdata scaling
CootAfter using ANODEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→79.39 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 26.622 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.524 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1109 1.7 %RANDOM
Rwork0.18041 ---
obs0.18089 62910 69.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.179 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.63 Å2-0 Å2
2---1.27 Å20 Å2
3---4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.62→79.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11504 732 110 108 12454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01712671
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611900
X-RAY DIFFRACTIONr_angle_refined_deg1.441.79617211
X-RAY DIFFRACTIONr_angle_other_deg0.4551.56927449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3595.2931534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.274206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.526102216
X-RAY DIFFRACTIONr_chiral_restr0.0610.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022726
X-RAY DIFFRACTIONr_mcbond_it1.5641.895783
X-RAY DIFFRACTIONr_mcbond_other1.5641.8895782
X-RAY DIFFRACTIONr_mcangle_it2.7183.3967236
X-RAY DIFFRACTIONr_mcangle_other2.7163.3947225
X-RAY DIFFRACTIONr_scbond_it2.0221.9096888
X-RAY DIFFRACTIONr_scbond_other2.0221.9096889
X-RAY DIFFRACTIONr_scangle_other2.8833.4259978
X-RAY DIFFRACTIONr_long_range_B_refined5.66217.7416097
X-RAY DIFFRACTIONr_long_range_B_other5.66217.7516094
LS refinement shellResolution: 2.622→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.117 3 -
Rwork0.348 359 -
obs--5.35 %
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)
11.09850.54230.01820.53340.03580.57460.00950.0303-0.16270.02620.0336-0.15130.05850.3033-0.04310.28740.02580.00290.3283-0.03820.0463-48.21560.882-36.312
21.15630.48910.090.53510.10020.43310.059-0.0450.24860.0172-0.02610.0751-0.29010.0126-0.03290.32380.00950.04020.2634-0.02360.0621-54.51367.731-0.033
37.7024-7.1735-0.465311.31531.29150.19440.0097-0.41281.1660.0281-0.086-0.3181-0.015-0.00750.07630.3223-0.1298-0.01750.4751-0.10020.3083-38.02470.336-35.605
45.32380.2692-1.19680.17930.12460.47650.24410.14041.2321-0.320.1618-0.0434-0.42270.1712-0.40590.7673-0.14870.29770.5603-0.01960.3603-33.77972.105-32.236
52.6509-2.3032-0.322611.04612.47650.59450.02350.4074-0.42750.13390.2653-1.14050.0230.2041-0.28880.233-0.0371-0.02960.5905-0.04360.355-41.472.8950.698
64.04911.4821-0.7652.87271.34441.27830.2033-0.3427-0.09360.15650.506-1.08410.02730.5242-0.70920.59350.1212-0.03230.5161-0.22340.484-37.98676.14-2.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A411 - 1485
2X-RAY DIFFRACTION2B411 - 1485
3X-RAY DIFFRACTION3E9 - 15
4X-RAY DIFFRACTION4F1 - 11
5X-RAY DIFFRACTION5G9 - 15
6X-RAY DIFFRACTION6H1 - 11

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