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- PDB-4z2e: Quinolone(Trovafloxacin)-DNA cleavage complex of gyrase from S. p... -

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Basic information

Entry
Database: PDB / ID: 4z2e
TitleQuinolone(Trovafloxacin)-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 type II (double strand cut, ATP-hydrolyzing) 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trovafloxacin / 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: 3.46 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)195,77212
Polymers194,8918
Non-polymers8814
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • octamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17240 Å2
ΔGint-139 kcal/mol
Surface area59940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.190, 96.620, 275.210
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, 6 molecules

#5: Chemical ChemComp-TR6 / Trovafloxacin / 7-[(1R,5S,6s)-6-amino-3-azabicyclo[3.1.0]hex-3-yl]-1-(2,4-difluorophenyl)-6-fluoro-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid / Trovafloxacin


Mass: 416.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15F3N4O3 / Comment: antibiotic*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.13 Å3/Da / Density % sol: 70.26 %
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: 3.37→56.045 Å / Num. obs: 36263 / % possible obs: 99.69 % / Redundancy: 6.66 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.3458
Reflection shellResolution: 3.37→3.46 Å / Redundancy: 6.75 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.28 / % possible all: 99.51

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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: 3.46→56.045 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 1620 4.84 %Random
Rwork0.2474 ---
obs0.2496 33472 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.46→56.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8898 765 62 2 9727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019971
X-RAY DIFFRACTIONf_angle_d0.45813803
X-RAY DIFFRACTIONf_dihedral_angle_d13.7453249
X-RAY DIFFRACTIONf_chiral_restr0.0271623
X-RAY DIFFRACTIONf_plane_restr0.0021719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.46-3.56180.44551200.30552596X-RAY DIFFRACTION99
3.5618-3.67670.36031440.27382575X-RAY DIFFRACTION99
3.6767-3.80810.30491510.2382598X-RAY DIFFRACTION100
3.8081-3.96060.26791560.22632604X-RAY DIFFRACTION99
3.9606-4.14080.25451300.21912639X-RAY DIFFRACTION100
4.1408-4.3590.27361240.2082638X-RAY DIFFRACTION100
4.359-4.6320.281290.22646X-RAY DIFFRACTION100
4.632-4.98940.2341220.21442676X-RAY DIFFRACTION100
4.9894-5.49110.30911180.24492669X-RAY DIFFRACTION100
5.4911-6.28480.34271490.29172673X-RAY DIFFRACTION100
6.2848-7.91460.29941180.28442750X-RAY DIFFRACTION100
7.9146-56.0450.2821590.25292788X-RAY DIFFRACTION98
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)
13.3424-0.1106-4.33.6111.76396.28620.17081.0582-0.45610.51370.16570.3142-1.3236-0.38510.08320.80330.1308-0.24091.216-0.09410.671572.40193.155236.8535
23.04251.7353-0.52783.0187-0.25012.18660.2204-0.3159-0.09160.1266-0.2835-0.0517-0.3548-0.05680.05980.8012-0.0336-0.10410.98770.01890.564386.3621-16.75139.8119
31.4761-1.4319-4.26691.24142.43067.78210.0772-0.5198-0.5669-0.68450.57170.1775-2.0947-0.84580.14030.7449-0.1567-0.16321.25540.05410.732780.9628-30.919516.7211
42.7011-2.0345-3.64867.09682.05647.38430.227-0.4778-0.19260.47180.21070.9920.809-2.1651-0.28140.8641-0.0075-0.04121.2565-0.06660.504790.9698-30.9701-9.8779
55.28583.1705-1.74325.2639-3.86385.83480.0959-1.3359-0.5648-0.3017-0.849-0.46890.28830.89311.00370.74350.0479-0.35710.77930.02790.702785.4614-40.866110.3056
66.14397.08165.39992.02218.49886.2750.59790.279-1.07471.06571.4219-2.73930.6070.8821-1.20691.1078-0.0545-0.11070.86090.0320.593283.8962-35.573433.5821
74.5724-0.04412.1174.74732.41852.21520.3198-0.10660.23180.4653-0.70590.39920.4766-0.14990.31731.7009-0.2910.05021.50370.22140.713497.0524-13.84270.2131
83.91982.3858-0.46929.2252-7.43646.68740.45520.82281.23351.0071-2.3121-0.6803-1.1669-0.17880.97540.93650.39540.07011.4479-0.2420.8799128.02895.068134.9438
92.40771.9311-2.34273.2195-0.08973.25960.26250.11650.2558-0.0941-0.00180.2367-0.9973-0.0957-0.23781.05510.11350.02880.59450.07410.5313113.109812.569616.0558
100.40311.26791.25374.09244.31413.86950.07370.2749-0.2313-0.6870.1573-0.9254-0.50710.24740.0041.46430.04850.09221.18970.16640.8432118.2532-6.3432-3.1596
118.20761.03392.75869.5913-3.25644.0135-0.01751.31230.1357-0.7807-1.0339-0.2201-0.78291.46480.81460.6110.04780.00150.7669-0.10830.5543108.2774-33.1605-9.5141
125.87884.64221.76295.78922.35523.9646-0.91071.52121.4399-0.83820.94092.0436-1.12320.1721-0.27571.5727-0.0855-0.07121.15380.3410.9453113.9842-10.3412-14.0593
138.4784-6.003-8.87964.33046.23569.21290.94720.54630.0856-0.8353-1.005-0.2679-0.65770.079-0.07531.6388-0.14780.15211.59730.10260.7446115.38411.2924-3.4775
146.162-0.734-0.40894.851-2.86982.77790.7658-0.2446-0.78540.1504-0.51590.7491.1145-0.0123-0.19551.14980.05680.0490.5343-0.10740.7312104.36939.507427.5233
152.0891-1.45880.24453.55230.71011.1195-0.1335-0.64530.4392-0.74-0.11540.4698-0.697-0.91230.25491.6010.5035-0.26791.4415-0.19720.905779.144518.960738.2544
163.89350.381.52141.23820.01052.60980.273-1.1657-0.62130.7958-0.1533-0.79650.1140.4925-0.1491.1636-0.1388-0.26161.1292-0.00170.8708121.05242.599650.3274
174.88852.81470.9812.6666-4.00125.14450.0348-1.7384-0.21360.3647-0.4326-0.8767-0.7190.26660.52671.39990.20240.08382.0243-0.1551.148686.56012.064449.3087
189.0410.7557-3.32482.3042-3.33616.3959-0.548-0.85410.204-1.44740.45860.76710.1731-0.53130.08541.55840.0582-0.2840.9871-0.13351.0917112.858716.459436.4641
190.9082-0.6983-0.40950.53270.30750.37560.0547-0.02360.0622-0.03640.08570.18620.0663-0.56630.10850.332-0.46580.61823.68860.09843.512108.51398.494341.2486
205.402-1.81692.57730.6292-1.09633.88020.62470.3309-0.43120.0290.2908-0.19280.55490.5949-0.71981.0326-0.9146-0.79513.60890.5610.685391.74798.488341.6725
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 1:10)
16X-RAY DIFFRACTION16(Chain C and (resseq 415:541 or resseq 585:648)) or (Chain A and resseq 1:10)
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 0 or resid 100)
20X-RAY DIFFRACTION20chain H and (resid 0 or resid 100)

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