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- PDB-6z1a: Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA -

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Basic information

Entry
Database: PDB / ID: 6z1a
TitleTernary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA
Components
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA gyrase subunit B,DNA gyrase subunit A
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR / FUSION PROTEIN
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-Q52 / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsKolaric, A. / Germe, T. / Hrast, M. / Stevenson, C.E.M. / Lawson, D.M. / Burton, N. / Voros, J. / Maxwell, A. / Minovski, N. / Anderluh, M.
Funding support Slovenia, United Kingdom, 4items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0017 Slovenia
Slovenian Research AgencyP1-0208 Slovenia
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
Wellcome Trust110072/Z/15/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds.
Authors: Kolaric, A. / Germe, T. / Hrast, M. / Stevenson, C.E.M. / Lawson, D.M. / Burton, N.P. / Voros, J. / Maxwell, A. / Minovski, N. / Anderluh, M.
History
DepositionMay 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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,DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit A
E: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')
F: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')
G: DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
H: DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,71517
Polymers168,3386
Non-polymers1,37711
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-67 kcal/mol
Surface area56000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.592, 92.592, 405.464
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12G
22H

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
11LYSLYSGLNGLNBA417 - 14899 - 690
21LYSLYSGLNGLNDB417 - 14899 - 690
12DGDGDTDTGE2009 - 20201 - 12
22DGDGDTDTHF2009 - 20201 - 12

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules BD

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


Mass: 78078.977 Da / Num. of mol.: 2 / Mutation: Y1123F
Source method: isolated from a genetically manipulated source
Details: Fusion of fragments taken from C-terminal domain of GyrB (residues 410-543 and 580-644) to N-terminal domain of GyrA (residues 2-491). For the GyrB component, deletion of residues 544-579 ...Details: Fusion of fragments taken from C-terminal domain of GyrB (residues 410-543 and 580-644) to N-terminal domain of GyrA (residues 2-491). For the GyrB component, deletion of residues 544-579 removes a Greek key motif. The deleted sequence is replaced by 2 residues: TG. For the GyrA component, the sequence numbering is advanced by 1000 in the coordinate file.,Fusion of fragments taken from C-terminal domain of GyrB (residues 410-543 and 580-644) to N-terminal domain of GyrA (residues 2-491). For the GyrB component, deletion of residues 544-579 removes a Greek key motif. The deleted sequence is replaced by 2 residues: TG. For the GyrA component, the sequence numbering is advanced by 1000 in the coordinate file.,Fusion of fragments taken from C-terminal domain of GyrB (residues 410-543 and 580-644) to N-terminal domain of GyrA (residues 2-491). For the GyrB component, deletion of residues 544-579 removes a Greek key motif. The deleted sequence is replaced by 2 residues: TG. For the GyrA component, the sequence numbering is advanced by 1000 in the coordinate file.,Fusion of fragments taken from C-terminal domain of GyrB (residues 410-543 and 580-644) to N-terminal domain of GyrA (residues 2-491). For the GyrB component, deletion of residues 544-579 removes a Greek key motif. The deleted sequence is replaced by 2 residues: TG. For the GyrA component, the sequence numbering is advanced by 1000 in the coordinate file.
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, gyrA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A0K8, UniProt: P20831, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 2 types, 4 molecules EFGH

#2: DNA chain DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')


Mass: 2451.630 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus N315 (bacteria)
#3: DNA chain DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 3638.379 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus N315 (bacteria)

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Non-polymers , 6 types, 354 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-Q52 / ~{N}-[(4-chlorophenyl)methyl]-1-[2-(6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-amine


Mass: 410.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27ClN4O / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→81.09 Å / Num. obs: 86845 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 41.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.043 / Rrim(I) all: 0.198 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3415.62.0177092845460.5570.522.0851.499.5
12.17-81.0919.60.0361213961810.0080.03751.6100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
REFMAC5.8.0258phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2XCS

2xcs


Resolution: 2.3→80.32 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.287 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2434 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 4484 5.2 %RANDOM
Rwork0.179 ---
obs0.181 82229 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.22 Å2 / Biso mean: 45.492 Å2 / Biso min: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.27 Å2-0 Å2
2---0.53 Å20 Å2
3---1.72 Å2
Refinement stepCycle: final / Resolution: 2.3→80.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10548 801 76 347 11772
Biso mean--73.94 44.01 -
Num. residues----1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311714
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710747
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.60615936
X-RAY DIFFRACTIONr_angle_other_deg1.3581.63924834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67551344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19221.184642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.068151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.82215116
X-RAY DIFFRACTIONr_chiral_restr0.0810.21544
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022510
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B211080.09
12D211080.09
21G8220.13
22H8220.13
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 348 -
Rwork0.278 6047 -
all-6395 -
obs--99.5 %
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)
13.0916-0.2469-2.04311.5509-0.19181.88770.1665-0.150.35190.13830.01170.1853-0.2751-0.1532-0.17820.1780.00250.04440.1822-0.08170.142215.049957.491562.4937
26.0186-0.2314-2.04670.5902-0.4212.0701-0.0749-0.4039-0.45930.24860.0199-0.03540.12230.12670.0550.2421-0.0102-0.02690.1837-0.02350.110922.985846.279565.5033
30.6534-0.0617-0.05970.872-0.27611.5940.01380.029-0.10370.00520.01390.0489-0.1106-0.013-0.02770.0308-0.00560.02150.0103-0.02110.056829.502936.871131.1267
42.08342.2999-1.00323.2183-1.54681.0414-0.032-0.0778-0.4752-0.0059-0.0308-0.45570.0862-0.08010.06280.16160.0199-0.02220.1033-0.00920.250221.5064-2.10640.2625
54.0839-0.423-1.15261.09960.46511.6520.09170.52490.3165-0.20.0238-0.0215-0.2425-0.1108-0.11550.27580.06920.02750.23640.12040.0968-4.605453.169216.6427
61.76480.3343-0.36740.7978-0.01921.3172-0.0122-0.0207-0.2078-0.07110.0197-0.0950.0790.1446-0.00750.06790.02470.01380.0221-0.00230.0496-14.417332.85644.8264
71.8480.7061.41622.30781.44563.8731-0.0788-0.08030.2063-0.1637-0.10520.0676-0.52430.05490.1840.12990.01310.0270.0340.0180.0564-20.44757.740761.5296
80.3804-0.8521-0.05862.5750.27050.07820.04070.0507-0.1639-0.0661-0.06780.23490.0654-0.00320.02710.1193-0.01740.02050.0784-0.01050.127-17.9526.815443.986
94.42581.7170.35864.40870.42380.0595-0.2270.20990.4847-0.73560.18470.4027-0.08140.05340.04230.1467-0.0725-0.03360.1057-0.01410.120424.717348.875140.0682
105.8979-2.1488-2.23776.9821.36255.0117-0.0712-0.16020.93070.58210.0581-0.254-0.3898-0.04150.01310.11580.0436-0.03540.13520.01630.2009-11.669552.110139.9643
119.4483-2.96594.43754.90870.56213.5137-0.2553-0.54640.1633-0.2320.4316-0.0764-0.4496-0.7522-0.17630.1683-0.01520.00860.1849-0.02670.26026.172351.604244.1723
126.3523-0.0817-0.82863.3393-0.42012.0236-0.0148-0.50630.57340.2765-0.00630.0484-0.33580.06490.02110.16370.05320.00730.1003-0.00060.1009-15.802955.008137.0145
131.1579-2.34012.4574.776-5.14035.8729-0.02950.16940.18460.2079-0.3093-0.3631-0.63660.25990.33880.5320.00660.02580.3415-0.06450.28657.066652.184735.0416
147.794-2.2404-0.9255.00660.2554.82070.21420.22320.3526-0.4894-0.0253-0.0457-0.32910.0707-0.18880.1418-0.03150.00390.02090.00520.041628.351451.308743.9242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B417 - 537
2X-RAY DIFFRACTION2B538 - 1018
3X-RAY DIFFRACTION3B1019 - 1365
4X-RAY DIFFRACTION4B1366 - 1491
5X-RAY DIFFRACTION5D416 - 1022
6X-RAY DIFFRACTION6D1023 - 1213
7X-RAY DIFFRACTION7D1214 - 1333
8X-RAY DIFFRACTION8D1334 - 1490
9X-RAY DIFFRACTION9E1 - 8
10X-RAY DIFFRACTION10F1 - 8
11X-RAY DIFFRACTION11G2009 - 2012
12X-RAY DIFFRACTION12G2013 - 2020
13X-RAY DIFFRACTION13H2009 - 2012
14X-RAY DIFFRACTION14H2013 - 2020

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