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- PDB-4z2d: Quinolone(Levofloxacin)-DNA cleavage complex of gyrase from S. pn... -

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Basic information

Entry
Database: PDB / ID: 4z2d
TitleQuinolone(Levofloxacin)-DNA cleavage complex of gyrase from S. pneumoniae
Components
  • (DNA gyrase subunit ...) x 2
  • (Symmetrized E-site ...) x 2
KeywordsISOMERASE / Gyrase / Cleavage complex / DNA / quinolone
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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, 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 superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LFX / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsLaponogov, I. / Veselkov, D.A. / Pan, X.-S. / Selvarajah, J. / Crevel, I.M.-T. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K010069/1 United Kingdom
CitationJournal: To Be Published
Title: Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae
Authors: Laponogov, I. / Veselkov, D.A. / Pan, X.-S. / Selvarajah, J. / Crevel, I.M.-T. / Fisher, L.M. / Sanderson, M.R.
History
DepositionMar 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit A
C: DNA gyrase subunit B
B: DNA gyrase subunit A
D: DNA gyrase subunit B
E: Symmetrized E-site DNA
F: Symmetrized E-site DNA
H: Symmetrized E-site DNA
G: Symmetrized E-site DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,66212
Polymers194,8918
Non-polymers7714
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18350 Å2
ΔGint-149 kcal/mol
Surface area57440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.130, 95.880, 275.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA gyrase subunit ... , 2 types, 4 molecules ABCD

#1: Protein DNA gyrase subunit A


Mass: 56747.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: gyrA, BM52_0349 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9R867, UniProt: Q8DPM2*PLUS, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B


Mass: 30286.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: gyrB, BM52_1967, DJ38_04430 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59957, UniProt: P0A4M0*PLUS, EC: 5.99.1.3

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Symmetrized E-site ... , 2 types, 4 molecules EGFH

#3: DNA chain Symmetrized E-site DNA


Mass: 4589.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain Symmetrized E-site DNA


Mass: 5821.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 12 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Source: (synth.) Escherichia coli (E. coli)
#6: Chemical ChemComp-LFX / (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid / Levofloxacin


Mass: 361.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20FN3O4 / Source: (synth.) Escherichia coli (E. coli)
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.98 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5-10% PEG 8000, 10-20% Ethylene glycol, 0.1M Imidazole/MES buffer system, 0.1M Amino Acids
PH range: 6.0-7.0 / Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.29→31.96 Å / Num. obs: 38701 / % possible obs: 99.81 % / Redundancy: 6.62 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.0912
Reflection shellResolution: 3.29→3.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.44 / % possible all: 99.67

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAF, 4I3H

3raf

4i3h


Resolution: 3.38→31.541 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 1727 4.84 %
Rwork0.2287 --
obs0.2312 35660 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.38→31.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9331 725 54 8 10118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310351
X-RAY DIFFRACTIONf_angle_d0.54214263
X-RAY DIFFRACTIONf_dihedral_angle_d13.2233534
X-RAY DIFFRACTIONf_chiral_restr0.0331676
X-RAY DIFFRACTIONf_plane_restr0.0031766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3801-3.47940.32711480.26652758X-RAY DIFFRACTION99
3.4794-3.59160.38681270.25222799X-RAY DIFFRACTION100
3.5916-3.71980.28461560.22952761X-RAY DIFFRACTION100
3.7198-3.86850.25391610.21772763X-RAY DIFFRACTION100
3.8685-4.04420.25081560.20342782X-RAY DIFFRACTION100
4.0442-4.25690.24851320.19492812X-RAY DIFFRACTION100
4.2569-4.52290.26661350.18792828X-RAY DIFFRACTION100
4.5229-4.8710.21361420.18952822X-RAY DIFFRACTION100
4.871-5.3590.29031180.21372868X-RAY DIFFRACTION100
5.359-6.12950.32631630.26292826X-RAY DIFFRACTION100
6.1295-7.70390.32461230.26982905X-RAY DIFFRACTION100
7.7039-31.54240.27191660.24063009X-RAY DIFFRACTION100
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)
19.0643-4.2534-6.09557.14083.69395.5015-0.5269-0.2416-0.2361.373-0.22630.0084-1.4119-0.1470.70271.02020.3185-0.25481.0606-0.09840.642572.19663.673937.0053
22.86391.44380.48733.0089-0.19712.96010.1756-0.1445-0.19870.1195-0.2453-0.0569-0.1775-0.36420.09010.70860.0325-0.08540.72580.0150.500686.2052-16.593139.8734
34.1551-1.9925-4.62863.75632.88625.26880.20540.3893-0.69-0.3588-0.51820.3291-0.6367-1.81490.35780.6494-0.1054-0.13090.8979-0.03470.723779.9812-30.662217.9626
46.3452-3.7282-2.47087.8148-1.66877.3450.0553-0.04590.1844-0.23930.50570.8742-0.0681-0.9432-0.56530.8032-0.1683-0.05990.9934-0.18150.606490.5296-31.0525-10.0521
52.46111.1048-3.47555.4579-4.9738.6413-0.112-1.0365-0.796-0.2807-1.1236-0.24330.10391.91341.0230.8483-0.0736-0.42010.99810.00080.843484.9426-40.759710.4691
69.23467.37426.67586.99735.9825.20770.99520.2229-1.82640.04410.4686-1.22440.5870.1114-1.51140.7824-0.0365-0.09320.70230.00070.644983.5844-35.299933.8656
78.18890.14461.9156.81664.26933.07950.7118-0.30020.19680.4287-0.5776-0.3266-0.02840.0325-0.1591.3017-0.09350.03191.03860.14840.601396.8666-13.158969.7901
81.62592.1189-2.13422.8778-2.99173.3380.05060.04440.67430.57310.20890.0523-1.44260.7143-0.16290.80780.2135-0.02180.7012-0.20490.7089127.33955.368234.6655
92.88181.1016-0.49072.4314-0.07832.5310.2793-0.29010.0664-0.04840.02970.2091-0.8323-0.0247-0.33661.23820.08370.10790.72910.03090.6724113.064412.905415.8291
101.87291.94112.24667.08675.37774.85340.25180.5002-0.3-0.21480.1191-1.1771-0.28650.3829-0.14151.045-0.05410.15211.02510.06710.7334117.8226-6.362-3.2679
115.84594.23832.72228.17990.45888.2458-0.3710.3248-0.0143-0.0298-0.3095-0.5467-1.00410.86660.56910.53770.02550.02390.6365-0.05240.6167107.8608-32.4308-9.2974
126.64815.88666.06225.23695.61598.0842-1.9132.07581.0138-1.66521.5141.1172-0.97630.29690.25531.18510.04660.06670.8230.05050.8382113.6036-10.0501-14.2272
138.2996-6.9291-8.03465.79666.78358.18611.53290.1465-0.2732-1.5155-0.9987-0.0016-1.4772-0.7335-0.53551.4628-0.12280.06940.69720.05850.6558115.032911.4811-3.6193
145.938-0.7778-2.47364.5303-0.11483.0684-0.0574-1.0365-0.13880.4417-0.07460.75830.24730.55570.16771.8406-0.0140.06450.7559-0.12721.08104.491739.287327.2292
151.5658-1.73170.73943.4963-0.07922.4659-0.0909-0.16480.5806-0.2837-0.10680.2188-1.1819-0.65210.19221.52330.556-0.25571.146-0.2350.798179.135619.410138.0955
161.0259-0.87520.71181.1455-0.36021.42710.1807-0.7643-0.25310.67590.0445-0.3220.21550.3952-0.2291.0693-0.1817-0.12491.0415-0.02340.659120.60712.590850.171
176.55020.89221.4196.0515-2.04284.9157-0.5903-2.2157-0.14490.2360.0956-0.6202-0.63380.65330.44411.22020.2688-0.05421.6624-0.14330.920386.98812.413548.1857
189.1885-0.1804-3.28462.4967-3.21645.4773-0.4445-1.26241.4842-0.3130.16560.4844-0.5571-0.0090.16151.5766-0.0609-0.30330.9377-0.19071.2349112.659716.794636.2908
190.0594-0.02820.02560.20640.39730.8789-0.06710.1879-0.473-0.12380.182-0.1710.05290.2519-0.01391.4224-0.60670.58463.4793-1.28313.767108.25039.713941.5701
205.09611.505-0.24761.0926-0.48392.04140.17780.56350.8404-0.39860.1051-1.0337-0.2481-0.1634-0.27811.6088-0.29240.00491.9456-0.87631.826491.63278.957242.5924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 11:32
2X-RAY DIFFRACTION2chain A and (resseq 33:240 or resseq 325:343 or resseq 478:486)
3X-RAY DIFFRACTION3chain A and resseq 344:386
4X-RAY DIFFRACTION4chain A and resseq 387:432
5X-RAY DIFFRACTION5chain A and resseq 433:457
6X-RAY DIFFRACTION6chain A and resseq 458:477
7X-RAY DIFFRACTION7chain A and resseq 241:324
8X-RAY DIFFRACTION8chain B and resseq 11:32
9X-RAY DIFFRACTION9chain B and (resseq 33:240 or resseq 325:343 or resseq 478:486)
10X-RAY DIFFRACTION10chain B and resseq 344:386
11X-RAY DIFFRACTION11chain B and resseq 387:432
12X-RAY DIFFRACTION12chain B and resseq 433:457
13X-RAY DIFFRACTION13chain B and resseq 458:477
14X-RAY DIFFRACTION14chain B and resseq 241:324
15X-RAY DIFFRACTION15(Chain D and (resseq 415:541 or resseq 585:648)) or (Chain B and resseq 2:10)
16X-RAY DIFFRACTION16(Chain C and (resseq 415:541 or resseq 585:648)) or (Chain A and resseq 2:10)
17X-RAY DIFFRACTION17(Chain E and resseq 7:15) or (Chain F and resseq 1:13)
18X-RAY DIFFRACTION18(Chain G and resseq 9:15) or (Chain H and resseq 1:11)
19X-RAY DIFFRACTION19Chain F and resid 101:102
20X-RAY DIFFRACTION20Chain H and resid 101:102

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