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- PDB-8c41: High resolution structure of the Streptococcus pneumoniae topoiso... -

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Basic information

Entry
Database: PDB / ID: 8c41
TitleHigh resolution structure of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin
Components
  • DNA (5'-D(*CP*AP*TP*GP*AP*AP*T)-3')
  • DNA (5'-D(*CP*GP*TP*GP*CP*AP*T)-3')
  • DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3')
  • DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3')
  • Fused ParE30ParC55 CLEAVAGE COMPLEX of the TOPOISOMERASE IV
KeywordsISOMERASE / PROTEIN-DNA CLEAVAGE COMPLEX / TOPOISOMERASE IIA / DELAFLOXACIN / TOPOISOMERASE IV-DNA-ANTIBIOTIC COMPLEX
Function / homologydelafloxacin / DNA / DNA (> 10)
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 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
DepositionDec 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fused ParE30ParC55 CLEAVAGE COMPLEX of the TOPOISOMERASE IV
B: Fused ParE30ParC55 CLEAVAGE COMPLEX of the TOPOISOMERASE IV
E: DNA (5'-D(*CP*AP*TP*GP*AP*AP*T)-3')
F: DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3')
G: DNA (5'-D(*CP*GP*TP*GP*CP*AP*T)-3')
H: DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,81719
Polymers179,3646
Non-polymers1,45313
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17990 Å2
ΔGint-164 kcal/mol
Surface area61200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.471, 157.471, 212.339
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-1774-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fused ParE30ParC55 CLEAVAGE COMPLEX of the TOPOISOMERASE IV


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 (residues 1001-1486)
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: 7785 / Gene: SP_0852-SP_0855 / Plasmid: PET29A / Production host: Escherichia coli (E. coli) / References: EC: 5.99.1.-

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DNA chain , 4 types, 4 molecules EFGH

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


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*G)-3')


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cleaved from the E18 mer oligo AGTCATTCATGACCTTGGT / Source: (synth.) DNA molecule (others)
#4: DNA chain DNA (5'-D(*CP*GP*TP*GP*CP*AP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#5: DNA chain DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*G)-3')


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Non-polymers , 5 types, 431 molecules

#6: 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
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5% Tacsimate, 50 mM Na Cacodylate, 62.5 mM KCl, 7.5 mM MgCl2, 4-7.5% Isopropanol. 30% MPD as cryoprotectant
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: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.393→115.01 Å / Num. obs: 70836 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 60.8 % / CC1/2: 1 / Rmerge(I) obs: 0.564 / Rpim(I) all: 0.073 / Rrim(I) all: 0.569 / Net I/σ(I): 8.4
Reflection shellResolution: 2.394→2.689 Å / Redundancy: 49.5 % / Rmerge(I) obs: 4.363 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3517 / CC1/2: 0.83 / Rpim(I) all: 0.62 / Rrim(I) all: 4.483 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB-REDOrefinement
DIALSdata reduction
xia2data reduction
Aimlessdata scaling
STARANISOv3.347 1-Sep-2022data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.393→115.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.175 / SU B: 14.946 / SU ML: 0.187 / Average fsc free: 0.9534 / Average fsc work: 0.9697 / Cross valid method: FREE R-VALUE / ESU R: 0.492 / ESU R Free: 0.307
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2432 3458 4.892 %
Rwork0.1922 67224 -
all0.195 --
obs-70682 58.857 %
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: 51.207 Å2
Baniso -1Baniso -2Baniso -3
1--0.489 Å2-0.244 Å2-0 Å2
2---0.489 Å20 Å2
3---1.586 Å2
Refinement stepCycle: LAST / Resolution: 2.393→115.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11462 732 92 418 12704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212573
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611491
X-RAY DIFFRACTIONr_angle_refined_deg1.541.66417121
X-RAY DIFFRACTIONr_angle_other_deg0.4771.56526821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65351442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.023591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.252102213
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.19210549
X-RAY DIFFRACTIONr_chiral_restr0.0710.21908
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022319
X-RAY DIFFRACTIONr_nbd_refined0.220.22612
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.211122
X-RAY DIFFRACTIONr_nbtor_refined0.1820.25945
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.26764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2413
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.213
X-RAY DIFFRACTIONr_nbd_other0.2310.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.28
X-RAY DIFFRACTIONr_mcbond_it2.832.495762
X-RAY DIFFRACTIONr_mcbond_other2.8292.495762
X-RAY DIFFRACTIONr_mcangle_it4.7113.7187200
X-RAY DIFFRACTIONr_mcangle_other4.713.7197201
X-RAY DIFFRACTIONr_scbond_it2.3862.6436811
X-RAY DIFFRACTIONr_scbond_other2.3862.6436811
X-RAY DIFFRACTIONr_scangle_it4.0673.8849915
X-RAY DIFFRACTIONr_scangle_other4.0673.8849916
X-RAY DIFFRACTIONr_lrange_it6.98227.6414351
X-RAY DIFFRACTIONr_lrange_other6.97227.59914328
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
2.393-2.4560.81100.2751990.29987800.8490.942.38040.291
2.456-2.5230.503300.355360.35786240.8990.9256.56310.363
2.523-2.5960.43480.3669720.36983000.9020.92812.28920.381
2.596-2.6760.392740.33513410.33881170.9140.94117.43260.33
2.676-2.7630.354840.31918280.32178400.9180.94224.38780.317
2.763-2.860.3731150.30322970.30676070.9080.94231.70760.294
2.86-2.9680.3211550.26528970.26873630.9350.95541.45050.253
2.968-3.0890.3362190.25942680.26370760.9340.95763.41150.24
3.089-3.2270.313140.2658630.26368220.9380.95890.54530.239
3.227-3.3840.2823190.23861190.2464840.9480.96599.29060.218
3.384-3.5670.2752990.2259100.22362240.950.97199.7590.201
3.567-3.7830.2443250.20454930.20658310.9610.97599.77710.187
3.783-4.0440.2412710.18152710.18355490.9650.9899.87390.167
4.044-4.3680.2172390.1649090.16351560.970.98499.84480.148
4.368-4.7840.1852100.14145480.14347600.980.98899.9580.133
4.784-5.3470.2072410.14940820.15343230.9770.9871000.14
5.347-6.1720.2171680.15636790.15938490.9730.98599.9480.148
6.172-7.5540.1831710.15231030.15432790.9780.98699.84750.145
7.554-10.660.145970.13224650.13325630.9870.98999.9610.128
10.66-115.010.268690.21814440.2215130.9410.9421000.26
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)
10.1489-0.0133-0.17360.02480.02860.3522-0.04610.00160.0085-0.03650.01660.06960.05410.13160.02950.31060.02240.0220.36130.00830.3217-47.096659.6239-36.4731
20.09380.0912-0.03910.1531-0.01010.16850.036-0.052-0.07260.013-0.02430.0332-0.0790.0447-0.01170.3470.00060.0140.33940.00850.3018-53.225667.7766-0.1111
32.3733-3.429-0.82244.97811.18940.2865-0.0533-0.15370.2430.03590.149-0.3301-0.00090.0563-0.09570.2905-0.0925-0.00910.4293-0.01560.1213-36.792369.0977-35.7169
43.54061.50031.62420.63990.69550.7592-0.0687-0.08960.3181-0.0133-0.03540.1217-0.00280.0280.10410.49090.04180.18480.5215-0.04710.1628-33.098370.2698-31.7423
51.9785-3.5979-0.51247.45640.86680.1384-0.0369-0.0506-0.0518-0.2184-0.0004-0.41230.03290.03470.03730.2971-0.09020.0570.42930.0420.3343-40.106472.863-0.292
64.6432.6801-2.7931.5591-1.60241.6959-0.0242-0.099-0.3177-0.0382-0.1131-0.2022-0.05490.07030.13730.46050.04440.01320.4268-0.12160.193-37.291875.7402-4.1765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA415 - 1486
2X-RAY DIFFRACTION2B415 - 1486
3X-RAY DIFFRACTION3E1 - 7
4X-RAY DIFFRACTION4F1 - 11
5X-RAY DIFFRACTION4F101
6X-RAY DIFFRACTION5G1 - 7
7X-RAY DIFFRACTION6H1 - 11
8X-RAY DIFFRACTION6H101

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