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- PDB-9foy: Ternary complex of a Mycobacterium tuberculosis DNA gyrase core f... -

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Basic information

Entry
Database: PDB / ID: 9foy
TitleTernary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b
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 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 / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKokot, M. / Hrast, M. / Feng, L. / Mitchenall, L.A. / Lawson, D.M. / Maxwell, A. / Minovski, N. / Anderluh, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006983/1 United Kingdom
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Structural Aspects of Mycobacterium tuberculosis DNA Gyrase Targeted by Novel Bacterial Topoisomerase Inhibitors.
Authors: Kokot, M. / Hrast Rambaher, M. / Feng, L. / Mitchenall, L.A. / Lawson, D.M. / Maxwell, A. / Parish, T. / Minovski, N. / Anderluh, M.
History
DepositionJun 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B,DNA gyrase subunit A
B: 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(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
G: DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-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)181,9618
Polymers180,9486
Non-polymers1,0132
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint-54 kcal/mol
Surface area63460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.041, 131.703, 96.281
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 84383.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion of C-terminal domain of GyrB (residues 426-675; UniProtKB entry P9WG45) to the N-terminal domain of GyrA (residues 2-500; UniProtKB entry P9WG47). In the coordinate file the fusion is ...Details: Fusion of C-terminal domain of GyrB (residues 426-675; UniProtKB entry P9WG45) to the N-terminal domain of GyrA (residues 2-500; UniProtKB entry P9WG47). In the coordinate file the fusion is treated as a single polypeptide chain. For the GyrB component, the numbering is relative to the full-length wild-type sequence, and for the GyrA component, the sequence numbering is advanced by 1000. Short non-native sequences SNA and IGSG are appended to the N- and C-termini of the fusion, respectively. There are two fusion polypeptides in the asymmetric unit corresponding to the biologically relevant assembly.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: gyrB, Rv0005, MTCY10H4.03, gyrA, Rv0006, MTCY10H4.04 / Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 PLYSS
References: UniProt: P9WG45, UniProt: P9WG47, DNA topoisomerase (ATP-hydrolysing)
#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: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Plasmid: PET-28B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 PLYSS
#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.) synthetic construct (others)
#4: Chemical ChemComp-A1ID8 / (1~{S})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol


Mass: 506.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26BrF2N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1ID9 / (1~{R})-2-[4-[[4-bromanyl-3,5-bis(fluoranyl)phenyl]methylamino]cyclohexyl]-1-(6-methoxy-1,5-naphthyridin-4-yl)ethanol


Mass: 506.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26BrF2N3O2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.06 Å3/Da / Density % sol: 59.9 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→69.23 Å / Num. obs: 50035 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.959 / Rmerge(I) obs: 0.414 / Rpim(I) all: 0.167 / Rrim(I) all: 0.447 / Χ2: 0.93 / Net I/σ(I): 4.9 / Num. measured all: 355596
Reflection shellResolution: 2.8→2.89 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.731 / Num. measured all: 31268 / Num. unique obs: 4567 / CC1/2: 0.414 / Rpim(I) all: 0.715 / Rrim(I) all: 1.875 / Χ2: 0.49 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→69.23 Å / Cor.coef. Fo:Fc: 0.846 / Cor.coef. Fo:Fc free: 0.816 / SU B: 30.465 / SU ML: 0.544 / Cross valid method: THROUGHOUT / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30408 2542 5.1 %RANDOM
Rwork0.27933 ---
obs0.28059 47469 99.99 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.024 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å2-0.86 Å2
2---2.05 Å20 Å2
3---4.31 Å2
Refinement stepCycle: 1 / Resolution: 2.8→69.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11438 814 64 0 12316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01312594
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511821
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.65217191
X-RAY DIFFRACTIONr_angle_other_deg1.221.58427116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44151454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62720.642701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.185152066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.60915136
X-RAY DIFFRACTIONr_chiral_restr0.0680.21690
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022854
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_it0.2484.4015834
X-RAY DIFFRACTIONr_mcbond_other0.2484.4015833
X-RAY DIFFRACTIONr_mcangle_it0.4666.6027282
X-RAY DIFFRACTIONr_mcangle_other0.4666.6027283
X-RAY DIFFRACTIONr_scbond_it0.1874.3596760
X-RAY DIFFRACTIONr_scbond_other0.1874.3596760
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3666.539910
X-RAY DIFFRACTIONr_long_range_B_refined1.85788528
X-RAY DIFFRACTIONr_long_range_B_other1.85788529
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)
11A237060.06
12B237060.06
21F9400.02
22H9400.02
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 212 -
Rwork0.37 3474 -
obs--100 %

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