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- PDB-6qx1: 2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA. -

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Basic information

Entry
Database: PDB / ID: 6qx1
Title2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
KeywordsISOMERASE / Inhibitor / DNA complex
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 / 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 / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus ...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
Similarity search - Domain/homology
GLYCINE / Chem-JK8 / : / DNA / DNA (> 10) / DNA gyrase subunit B / 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: 2.65 Å
AuthorsBax, B.D.
Funding support1items
OrganizationGrant numberCountry
European Union115583
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.
Authors: Thalji, R.K. / Raha, K. / Andreotti, D. / Checchia, A. / Cui, H. / Meneghelli, G. / Profeta, R. / Tonelli, F. / Tommasi, S. / Bakshi, T. / Donovan, B.T. / Howells, A. / Jain, S. / Nixon, C. ...Authors: Thalji, R.K. / Raha, K. / Andreotti, D. / Checchia, A. / Cui, H. / Meneghelli, G. / Profeta, R. / Tonelli, F. / Tommasi, S. / Bakshi, T. / Donovan, B.T. / Howells, A. / Jain, S. / Nixon, C. / Quinque, G. / McCloskey, L. / Bax, B.D. / Neu, M. / Chan, P.F. / Stavenger, R.A.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 24, 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_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
A: DNA gyrase subunit A
D: DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
F: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,96617
Polymers168,5566
Non-polymers1,41111
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22310 Å2
ΔGint-122 kcal/mol
Surface area56870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.190, 93.190, 408.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C
13E
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSTYRTYRBA417 - 6399 - 197
21LYSLYSTYRTYRDC417 - 6399 - 197
12ASNASNGLNGLNAB10 - 4899 - 488
22ASNASNGLNGLNCD10 - 4899 - 488
13DADADTDTEE1 - 20201 - 20
23DADADTDTFF1 - 20201 - 20

NCS ensembles :
ID
1
2
3

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Components

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

#1: Protein 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 (bacteria) / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli)
References: UniProt: P66937, UniProt: P0A0K8*PLUS, EC: 5.99.1.3
#2: Protein DNA gyrase subunit A


Mass: 55537.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / 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

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


Mass: 6134.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 6 types, 342 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-JK8 / (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine


Mass: 364.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.2 / Details: 11% PEG 5000MME, 150mM BisTris pH6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→58.43 Å / Num. obs: 57152 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Net I/σ(I): 12.4
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8352 / Rpim(I) all: 0.36 / Rrim(I) all: 0.645 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2XCS

2xcs


Resolution: 2.65→57.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 21.418 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.20615 2904 5.1 %RANDOM
Rwork0.16211 ---
obs0.16429 54124 98.38 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 60.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.65→57.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10582 807 89 331 11809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01211959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.60516325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50151360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01821.149653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.975152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.46615119
X-RAY DIFFRACTIONr_chiral_restr0.1410.21576
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.028929
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.643.6265422
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2185.4266785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7584.2236537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.75170.07252290
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B56590.12
12D56590.12
21A156070.1
22C156070.1
31E13970.15
32F13970.15
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 242 -
Rwork0.283 3974 -
obs--98.87 %
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)
11.36860.5357-0.60881.7052-0.32230.27790.0685-0.20570.123-0.0855-0.0140.2337-0.01350.1004-0.05450.28480.03130.01160.165-0.09730.231813.793654.55663.7754
20.2669-0.003-0.03870.3004-0.11830.44220.01310.086-0.11020.09680.02490.0458-0.07710.0447-0.0380.31510.02180.03170.1448-0.03020.255329.820629.099134.3635
33.03661.98431.25192.47210.19510.85010.02750.29-0.40290.27430.1308-0.4139-0.06330.1176-0.15830.33720.02850.01220.0473-0.0060.420728.2484-2.841139.6952
44.67720.1902-0.43230.3774-0.38320.4024-0.2192-0.0925-0.0802-0.06450.0864-0.14420.08-0.08850.13290.39750.00570.01150.0454-0.02090.204110.4554-13.697246.4422
51.1787-0.4008-0.74280.82291.47192.6507-0.1511-0.37390.03550.05840.1853-0.03690.18150.2947-0.03410.37710.05170.00180.2359-0.04350.145333.186447.702161.926
62.0819-1.2517-0.50071.4720.36720.12750.13270.39960.31770.1784-0.0626-0.3183-0.0209-0.0764-0.07010.34440.0278-0.01150.19690.12540.1954-0.446853.835615.4845
70.30890.1174-0.02670.20460.11850.3625-0.0077-0.1138-0.135-0.1465-0.0144-0.0307-0.1032-0.01440.02210.3510.05930.03490.1354-0.01770.2393-19.731933.479946.825
81.1033-1.0634-0.37642.2931-0.28571.95540.054-0.10520.0799-0.147-0.00780.06910.12110.0385-0.04620.34210.01180.0030.0503-0.09930.2982-21.60171.328744.9045
92.0285-0.28590.24010.7110.38740.5565-0.08780.024-0.0838-0.01250.03630.13490.00970.07180.05150.40450.00980.02690.0706-0.05390.1899-5.6633-12.496439.6072
101.2633-0.2765-1.10771.1519-0.882.1387-0.09790.4959-0.01150.1977-0.0299-0.0768-0.0081-0.45540.12780.37210.04720.01270.34930.04280.0317-20.64350.181917.8314
110.5774-0.5434-0.7191.4247-0.04561.5208-0.07370.0402-0.0352-0.08930.0790.10150.0037-0.1696-0.00520.473-0.0367-0.03720.0497-0.02090.240122.111850.89740.5354
121.18980.9057-1.27420.7283-0.84371.84610-0.1090.09170.0348-0.02110.086-0.05950.29180.0210.49370.1260.01090.1432-0.03670.2933-9.885753.689139.1495
130.04030.0119-0.13821.2725-0.14961.7101-0.06410.0337-0.05290.04320.00630.1206-0.2412-0.00740.05780.3962-0.0225-0.00140.153-0.04490.186331.131956.198813.7369
140.44120.58150.44711.24280.22551.2712-0.0201-0.1363-0.063-0.2184-0.1381-0.1436-0.3035-0.0910.15830.42520.02320.01730.1536-0.00310.2157-16.961761.877165.4565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B417 - 608
2X-RAY DIFFRACTION2A29 - 244
3X-RAY DIFFRACTION2A328 - 369
4X-RAY DIFFRACTION2A461 - 490
5X-RAY DIFFRACTION3A370 - 379
6X-RAY DIFFRACTION3A445 - 460
7X-RAY DIFFRACTION4A380 - 444
8X-RAY DIFFRACTION5A10 - 28
9X-RAY DIFFRACTION5B609 - 638
10X-RAY DIFFRACTION6D417 - 608
11X-RAY DIFFRACTION7C29 - 244
12X-RAY DIFFRACTION7C328 - 369
13X-RAY DIFFRACTION7C461 - 490
14X-RAY DIFFRACTION8C370 - 379
15X-RAY DIFFRACTION8C445 - 460
16X-RAY DIFFRACTION9C380 - 444
17X-RAY DIFFRACTION10C10 - 28
18X-RAY DIFFRACTION10D609 - 638
19X-RAY DIFFRACTION11E1 - 8
20X-RAY DIFFRACTION11F2009 - 2019
21X-RAY DIFFRACTION12E2009 - 2020
22X-RAY DIFFRACTION12F1 - 8
23X-RAY DIFFRACTION13A245 - 327
24X-RAY DIFFRACTION14C245 - 327

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