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- PDB-9fz6: A 2.58A crystal structure of S. aureus DNA gyrase and DNA with me... -

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Basic information

Entry
Database: PDB / ID: 9fz6
TitleA 2.58A crystal structure of S. aureus DNA gyrase and DNA with metals identified through anomalous scattering
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3')
  • DNA (5'-D(*AP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
KeywordsISOMERASE / Type IIA Topoisomerase / DNA / Metals
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 / 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
: / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsMorgan, H. / Duman, R. / Bax, B.D. / Warren, A.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2024
Title: How Do Gepotidacin and Zoliflodacin Stabilize DNA Cleavage Complexes with Bacterial Type IIA Topoisomerases? 1. Experimental Definition of Metal Binding Sites.
Authors: Morgan, H. / Nicholls, R.A. / Warren, A.J. / Ward, S.E. / Evans, G. / Long, F. / Murshudov, G.N. / Duman, R. / Bax, B.D.
History
DepositionJul 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)166,76121
Polymers165,6328
Non-polymers1,12913
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22840 Å2
ΔGint-139 kcal/mol
Surface area57470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.633, 93.633, 410.874
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 ... , 2 types, 4 molecules ACBD

#1: Protein DNA gyrase subunit A


Mass: 54738.453 Da / Num. of mol.: 2 / Mutation: Y123F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA / Production host: Escherichia coli (E. coli)
References: UniProt: P20831, DNA topoisomerase (ATP-hydrolysing)
#2: Protein DNA gyrase subunit B


Mass: 21345.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Production host: Escherichia coli (E. coli)
References: UniProt: P0A0K8, DNA topoisomerase (ATP-hydrolysing)

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DNA chain , 2 types, 4 molecules EFGH

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


Mass: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Non-polymers , 4 types, 350 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.13 Å3/Da / Density % sol: 60.75 % / Description: Twinned hexagonal rod
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 6.1
Details: PEG 5000 MME, 150 mM BisTris pH 6.1, 20 mM HEPES pH 7.0
Temp details: Room temperature incubation

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 1.8785 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jan 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8785 Å / Relative weight: 1
ReflectionResolution: 2.58→57.72 Å / Num. obs: 63516 / % possible obs: 100 % / Redundancy: 55.4 % / Biso Wilson estimate: 60.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.231 / Rpim(I) all: 0.031 / Rrim(I) all: 0.233 / Χ2: 0.92 / Net I/σ(I): 22.1
Reflection shellResolution: 2.58→2.74 Å / % possible obs: 99.1 % / Redundancy: 31.3 % / Rmerge(I) obs: 3.783 / Num. measured all: 319075 / Num. unique obs: 10183 / CC1/2: 0.542 / Rpim(I) all: 0.619 / Rrim(I) all: 3.836 / Χ2: 0.8 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
REFMAC5.8.0425refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→57.72 Å / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 22.4 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1997 6287 4.97 %
Rwork0.1401 --
obs0.1522 63403 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→57.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10615 793 58 337 11803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811867
X-RAY DIFFRACTIONf_angle_d1.2816171
X-RAY DIFFRACTIONf_dihedral_angle_d16.5584683
X-RAY DIFFRACTIONf_chiral_restr0.0711811
X-RAY DIFFRACTIONf_plane_restr0.0111992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.630.3462720.21815786X-RAY DIFFRACTION93
2.63-2.670.33512460.22566208X-RAY DIFFRACTION96
2.67-2.720.3212900.21245955X-RAY DIFFRACTION95
2.72-2.780.3143030.2016014X-RAY DIFFRACTION95
2.78-2.840.27313190.19476132X-RAY DIFFRACTION95
2.84-2.910.29423480.20245919X-RAY DIFFRACTION94
2.91-2.980.29593100.18296009X-RAY DIFFRACTION95
2.98-3.060.2463600.19345985X-RAY DIFFRACTION94
3.06-3.150.27043640.1795928X-RAY DIFFRACTION94
3.15-3.250.21582980.16856075X-RAY DIFFRACTION95
3.25-3.370.21532780.16546047X-RAY DIFFRACTION96
3.37-3.50.23223360.17265973X-RAY DIFFRACTION95
3.5-3.660.20773240.16666030X-RAY DIFFRACTION95
3.66-3.860.21743200.15476027X-RAY DIFFRACTION95
3.86-4.10.21873760.15245963X-RAY DIFFRACTION94
4.1-4.410.18133020.13216004X-RAY DIFFRACTION95
4.41-4.860.15233000.11776027X-RAY DIFFRACTION95
4.86-5.560.1813540.12055999X-RAY DIFFRACTION94
5.56-70.15743000.1246023X-RAY DIFFRACTION95
7-57.720.17622870.13086047X-RAY DIFFRACTION95

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