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- PDB-6fqs: 3.11A complex of S.Aureus gyrase with imidazopyrazinone T3 and DNA -

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Basic information

Entry
Database: PDB / ID: 6fqs
Title3.11A complex of S.Aureus gyrase with imidazopyrazinone T3 and DNA
Components
  • (DNA gyrase subunit ...) x 3
  • DNA (5'-D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*TP*T)-3')
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR
Function / homology
Function and homology information


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 / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / 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
Chem-E3E / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.11 Å
AuthorsBax, B.D. / Germe, T. / Basque, E. / Maxwell, A.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative Joint Undertaking115583
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.
Authors: Germe, T. / Voros, J. / Jeannot, F. / Taillier, T. / Stavenger, R.A. / Bacque, E. / Maxwell, A. / Bax, B.D.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA gyrase subunit B,DNA gyrase subunit B
A: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*TP*T)-3')
F: DNA (5'-D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,27020
Polymers168,6646
Non-polymers1,60614
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22880 Å2
ΔGint-146 kcal/mol
Surface area58130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.027, 94.027, 420.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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DNA gyrase subunit ... , 3 types, 4 molecules BDAC

#1: Protein DNA gyrase subunit B,DNA gyrase subunit B


Mass: 22605.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3
#2: Protein DNA gyrase subunit A


Mass: 55537.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#3: Protein DNA gyrase subunit A


Mass: 55617.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3

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DNA chain , 1 types, 2 molecules EF

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


Mass: 6148.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 126 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-E3E / 5-cyclopropyl-8-fluoranyl-7-pyridin-4-yl-imidazo[1,2-a]quinoxalin-4-one


Mass: 320.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13FN4O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 8% PEG 5000 MME, 90 mM bis-tris pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.11→48 Å / Num. obs: 37639 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.194 / Net I/σ(I): 9.5
Reflection shellResolution: 3.11→3.22 Å / Rmerge(I) obs: 1.572 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3666 / CC1/2: 0.532

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5CDM

5cdm


Resolution: 3.11→47.014 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.98
RfactorNum. reflection% reflection
Rfree0.21 1843 4.91 %
Rwork0.1788 --
obs0.1803 37524 99.92 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Refinement stepCycle: LAST / Resolution: 3.11→47.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10526 809 104 112 11551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112047
X-RAY DIFFRACTIONf_angle_d1.31116481
X-RAY DIFFRACTIONf_dihedral_angle_d20.3327378
X-RAY DIFFRACTIONf_chiral_restr0.0651838
X-RAY DIFFRACTIONf_plane_restr0.0072017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.19410.33421490.28832716X-RAY DIFFRACTION99
3.1941-3.28810.34481530.2622709X-RAY DIFFRACTION100
3.2881-3.39420.271320.24282784X-RAY DIFFRACTION100
3.3942-3.51540.23331200.23712743X-RAY DIFFRACTION100
3.5154-3.65610.24341630.19492734X-RAY DIFFRACTION100
3.6561-3.82250.21331400.17582731X-RAY DIFFRACTION100
3.8225-4.02390.21031560.16382737X-RAY DIFFRACTION100
4.0239-4.27580.18681620.16372759X-RAY DIFFRACTION100
4.2758-4.60570.17121320.13892730X-RAY DIFFRACTION100
4.6057-5.06870.18681390.14092750X-RAY DIFFRACTION100
5.0687-5.8010.19951350.17372748X-RAY DIFFRACTION100
5.801-7.30420.21741270.19772790X-RAY DIFFRACTION100
7.3042-47.01880.18321350.16792750X-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)
12.2498-2.34830.62371.8680.29181.2489-0.1444-0.3681-0.1860.75030.0930.75010.2167-0.458601.1527-0.14910.10690.5674-0.14570.633116.167854.194864.1041
20.206-0.0989-0.2548-0.10370.20750.152-0.2188-0.45930.22350.2633-0.0105-0.478-0.02670.341601.0858-0.1021-0.09080.701-0.04650.580735.276848.512960.9185
32.155-0.0163-0.40852.65590.22481.1027-0.02640.0378-0.23650.2245-0.09160.06260.0437-0.0553-00.6282-0.15-0.0170.2861-0.03840.411129.534328.75134.3436
42.1467-0.44140.58410.823500.7919-0.24640.30430.41270.29260.13470.0159-0.6125-0.262900.8435-0.1739-0.0410.480.00960.493729.937256.617214.4408
50.13350.10170.07830.0948-0.10850.02870.08090.043-0.38890.06150.0063-0.2061-0.0814-0.0256-00.7801-0.05-0.02630.41250.08720.723526.431-3.973638.5509
61.52910.4068-0.11660.5719-0.31190.2499-0.2019-0.1063-0.453-0.0274-0.0645-0.22020.04420.0152-00.8678-0.0927-0.03710.31050.02440.574110.485-14.483346.7188
71.35950.1549-0.18970.13350.43930.1221-0.4931.1888-0.0063-0.23941.1434-0.6804-0.00080.7316-01.34-0.05810.11311.24440.76630.6839-3.560353.802817.9581
80.28660.0351-0.09270.1946-0.10340.0145-0.09030.82120.6294-0.2142-0.14090.1622-0.0051-0.168301.0860.0872-0.02941.15340.20040.7572-23.260950.99920.7744
91.9645-0.1723-0.44122.96390.00081.3545-0.00310.0972-0.2881-0.0743-0.1212-0.10030.08240.216800.42720.0369-0.02590.19130.0160.2677-20.449432.56148.8913
101.76690.7630.69360.6040.11391.075-0.2513-0.21990.29720.14980.14960.0519-0.35380.2492-00.89890.021-0.10090.40560.0170.5273-18.520161.713567.2422
110.1789-0.03450.16750.22370.1560.11830.2673-0.52760.6407-0.05590.0255-0.1538-0.08970.1332-00.9474-0.0483-0.02440.3783-0.1290.6498-20.0323-0.475947.0267
121.6578-0.0675-0.27330.81560.15210.4053-0.15090.0451-0.0666-0.1085-0.059-0.06890.1094-0.034400.9357-0.0816-0.03340.3299-0.03080.513-5.2492-13.579639.6206
13-0.1921-0.1922-0.08770.28810.06610.1648-0.2082-0.00240.06910.27210.0920.1944-0.0779-0.05500.8797-0.124-0.00410.438-0.00310.680726.337849.460642.6359
14-0.00880.43440.14020.5532-0.28380.0263-0.11290.070.86640.1099-0.1688-0.6-0.1533-0.191800.84370.1023-0.0280.5460.18260.9838-14.282852.115239.2209
15-0.1380.11280.02520.0008-0.02290.1219-0.24410.0252-0.17010.54420.3281.0598-1.542-0.1757-01.02270.0902-0.03451.0309-0.04511.14344.122552.640940.6715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain B and (resid 445:605)))
2X-RAY DIFFRACTION2((chain A and (resid 14:25)) or (chain B and (resid 609:635)))
3X-RAY DIFFRACTION3((chain A and (resid 34:244 or resid 328:369 or resid 458:488)))
4X-RAY DIFFRACTION4((chain A and (resid 245:327)))
5X-RAY DIFFRACTION5((chain A and (resid 370:379 or resid 443:457)))
6X-RAY DIFFRACTION6((chain A and (resid 380:442)))
7X-RAY DIFFRACTION7((chain D and (resid 445:605)) or (chain G and (resid 201:224)))
8X-RAY DIFFRACTION8((chain C and (resid 14:25)) or (chain D and (resid 609:635)))
9X-RAY DIFFRACTION9((chain C and (resid 34:244 or resid 328:369 or resid 458:488)))
10X-RAY DIFFRACTION10((chain C and (resid 245:327)))
11X-RAY DIFFRACTION11((chain C and (resid 370:379 or resid 443:457)))
12X-RAY DIFFRACTION12((chain C and (resid 380:442)))
13X-RAY DIFFRACTION13((chain E and (resid -7:-1)) or (chain F and (resid 5:11)))
14X-RAY DIFFRACTION14((chain E and (resid 5:11)) or (chain F and (resid -7:-1)))
15X-RAY DIFFRACTION15((chain E and (resid 1:4)) or (chain F and (resid 1:4)) or (chain I and (resid 1:201)))

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