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- PDB-7ugw: M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin -

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Basic information

Entry
Database: PDB / ID: 7ugw
TitleM. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin
Components
  • DNA (46-MER)
  • DNA gyrase subunit A
  • DNA gyrase subunit B
  • evybactin
KeywordsISOMERASE/ANTIBIOTIC/DNA / Topoisomerase / inhibitor / natural product / ISOMERASE-ANTIBIOTIC-DNA complex
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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...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 / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / 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 / 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 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 / EF-hand calcium-binding domain. / 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 speciesMycobacterium tuberculosis H37Rv (bacteria)
Photorhabdus noenieputensis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHauk, G. / Imai, Y. / Lewis, K. / Berger, J.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI118687 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA077373 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35263778 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis.
Authors: Imai, Y. / Hauk, G. / Quigley, J. / Liang, L. / Son, S. / Ghiglieri, M. / Gates, M.F. / Morrissette, M. / Shahsavari, N. / Niles, S. / Baldisseri, D. / Honrao, C. / Ma, X. / Guo, J.J. / Berger, J.M. / Lewis, K.
History
DepositionMar 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
V: DNA (46-MER)
E: evybactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,7848
Polymers183,7366
Non-polymers492
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.075, 105.088, 250.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA gyrase subunit A / / Type IIA topoisomerase subunit GyrA


Mass: 55870.184 Da / Num. of mol.: 2 / Mutation: Y129F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrA, Rv0006, MTCY10H4.04 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WG47, DNA topoisomerase (ATP-hydrolysing)
#2: Protein DNA gyrase subunit B /


Mass: 28129.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: gyrB, Rv0005, MTCY10H4.03 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WG45, DNA topoisomerase (ATP-hydrolysing)
#3: DNA chain DNA (46-MER)


Mass: 14228.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein/peptide evybactin


Type: Peptide-like / Class: Antibiotic / Mass: 1508.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Photorhabdus noenieputensis (bacteria) / References: BIRD: PRD_002496
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7-12% PEG10K; 100mM MES pH 6.0; 200mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3→48.46 Å / Num. obs: 44612 / % possible obs: 99.64 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1395 / Rpim(I) all: 0.06624 / Rrim(I) all: 0.1549 / Net I/σ(I): 10.44
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 4388 / CC1/2: 0.822

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BS8

5bs8


Resolution: 3→44.46 Å / SU ML: 0.4872 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 1809 4.06 %
Rwork0.2011 42775 -
obs0.2044 44612 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.03 Å2
Refinement stepCycle: LAST / Resolution: 3→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11321 945 108 0 12374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013112664
X-RAY DIFFRACTIONf_angle_d1.554917331
X-RAY DIFFRACTIONf_chiral_restr0.06981965
X-RAY DIFFRACTIONf_plane_restr0.01062126
X-RAY DIFFRACTIONf_dihedral_angle_d20.91044830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.4831370.3153237X-RAY DIFFRACTION99.73
3.08-3.170.35681360.27333218X-RAY DIFFRACTION99.79
3.17-3.270.32241390.24713261X-RAY DIFFRACTION99.71
3.27-3.390.33461350.23313223X-RAY DIFFRACTION99.53
3.39-3.530.32611390.21523274X-RAY DIFFRACTION99.82
3.53-3.690.28251360.20773218X-RAY DIFFRACTION99.67
3.69-3.880.2861390.19693300X-RAY DIFFRACTION99.42
3.88-4.120.28331390.18433253X-RAY DIFFRACTION99.74
4.12-4.440.28071380.1683283X-RAY DIFFRACTION99.59
4.44-4.890.24771410.16393321X-RAY DIFFRACTION99.68
4.89-5.590.23691390.17793305X-RAY DIFFRACTION99.77
5.6-7.040.28511420.2073376X-RAY DIFFRACTION99.72
7.05-44.460.24931490.19623506X-RAY DIFFRACTION99.78

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