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- EMDB-19782: M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403 -
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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403 | ||||||||||||
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![]() | Mycobacterium tuberculosis / DNA gyrase / Novel Bacterial Topoisomerase II Inhibitors / antibiotic resistance / structure-activity relation / DNA BINDING PROTEIN | ||||||||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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 | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
![]() | Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E ...Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Gubellini F / Mechaly A / Alzari PM / Deprez B / Baulard A / Aubry A / Willand N / Petrella S | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403 Authors: Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Gubellini F / Mechaly A / Alzari PM / Deprez B / Baulard A / Aubry ...Authors: Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Gubellini F / Mechaly A / Alzari PM / Deprez B / Baulard A / Aubry A / Willand N / Petrella S | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 108.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.2 KB 25.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.6 KB | Display | ![]() |
Images | ![]() | 53.2 KB | ||
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() ![]() | 189.1 MB 200.3 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 165.5 KB | Display | ![]() |
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Full document | ![]() | 165 KB | Display | |
Data in XML | ![]() | 573 B | Display | |
Data in CIF | ![]() | 483 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s7oMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_19782_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19782_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19782_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403
Entire | Name: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403 |
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Components |
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-Supramolecule #1: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403
Supramolecule | Name: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: DNA gyrase
Supramolecule | Name: DNA gyrase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: DNA gyrase subunit A
Macromolecule | Name: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing) |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 92.30418 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: TDTTLPPDDS LDRIEPVDIE QEMQRSYIDY AMSVIVGRAL PEVRDGLKPV HRRVLYAMFD SGFRPDRSHA KSARSVAETM GNYHPHGDA SIYDSLVRMA QPWSLRYPLV DGQGNFGSPG NDPPAAMRYT EARLTPLAME MLREIDEETV DFIPNYDGRV Q EPTVLPSR ...String: TDTTLPPDDS LDRIEPVDIE QEMQRSYIDY AMSVIVGRAL PEVRDGLKPV HRRVLYAMFD SGFRPDRSHA KSARSVAETM GNYHPHGDA SIYDSLVRMA QPWSLRYPLV DGQGNFGSPG NDPPAAMRYT EARLTPLAME MLREIDEETV DFIPNYDGRV Q EPTVLPSR FPNLLANGSG GIAVGMATNI PPHNLRELAD AVFWALENHD ADEEETLAAV MGRVKGPDFP TAGLIVGSQG TA DAYKTGR GSIRMRGVVE VEEDSRGRTS LVITELPYQV NHDNFITSIA EQVRDGKLAG ISNIEDQSSD RVGLRIVIEI KRD AVAKVV INNLYKHTQL QTSFGANMLA IVDGVPRTLR LDQLIRYYVD HQLDVIVRRT TYRLRKANER AHILRGLVKA LDAL DEVIA LIRASETVDI ARAGLIELLD IDEIQAQAIL DMQLRRLAAL ERQRIIDDLA KIEAEIADLE DILAKPERQR GIVRD ELAE IVDRHGDDRR TRIIAIDGDV SDEDLIARED VVVTITETGY AKRTKTDLYR SQKRGGKGVQ GAGLKQDDIV AHFFVC STH DLILFFTTQG RVYRAKAYDL PEASRTARGQ HVANLLAFQP EERIAQVIQI RGYTDAPYLV LATRNGLVKK SKLTDFD SN RSGGIVAVNL RDNDELVGAV LCSAGDDLLL VSANGQSIRF SATDEALRPM GRATSGVQGM RFNIDDRLLS LNVVREGT Y LLVATSGGYA KRTAIEEYPV QGRGGKGVLT VMYDRRRGRL VGALIVDDDS ELYAVTSGGG VIRTAARQVR KAGRQTKGV RLMNLGEGDT LLAIARNAEE SGDDNAVDAN GADQTGN UniProtKB: DNA gyrase subunit A |
-Macromolecule #2: DNA gyrase subunit B
Macromolecule | Name: DNA gyrase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing) |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 74.423953 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAMVAAQKKK AQDEYGAASI TILEGLEAVR KRPGMYIGST GERGLHHLIW EVVDNAVDEA MAGYATTVNV VLLEDGGVEV ADDGRGIPV ATHASGIPTV DVVMTQLHAG GKFDSDAYAI SGGLHGVGVS VVNALSTRLE VEIKRDGYEW SQVYEKSEPL G LKQGAPTK ...String: GAMVAAQKKK AQDEYGAASI TILEGLEAVR KRPGMYIGST GERGLHHLIW EVVDNAVDEA MAGYATTVNV VLLEDGGVEV ADDGRGIPV ATHASGIPTV DVVMTQLHAG GKFDSDAYAI SGGLHGVGVS VVNALSTRLE VEIKRDGYEW SQVYEKSEPL G LKQGAPTK KTGSTVRFWA DPAVFETTEY DFETVARRLQ EMAFLNKGLT INLTDERVTQ DEVVDEVVSD VAEAPKSASE RA AESTAPH KVKSRTFHYP GGLVDFVKHI NRTKNAIHSS IVDFSGKGTG HEVEIAMQWN AGYSESVHTF ANTINTHEGG THE EGFRSA LTSVVNKYAK DRKLLKDKDP NLTGDDIREG LAAVISVKVS EPQFEGQTKT KLGNTEVKSF VQKVCNEQLT HWFE ANPTD AKVVVNKAVS SAQARIAARK ARELVRRKSA TDIGGLPGKL ADCRSTDPRK SELYVVEGDS AGGSAKSGRD SMFQA ILPL RGKIINVEKA RIDRVLKNTE VQAIITALGT GIHDEFDIGK LRYHKIVLMA DADVDGQHIS TLLLTLLFRF MRPLIE NGH VFLAQPPLYK LKWQRSDPEF AYSDRERDGL LEAGLKAGKK INKEDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVT LD DAAAADELFS ILMGEDVDAR RSFITRNAKD VRFLDV UniProtKB: DNA gyrase subunit B |
-Macromolecule #3: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
Macromolecule | Name: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 46.325371 KDa |
Sequence | String: (DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DT) (DA)(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DC) (DT)(DC)(DT)(DT)(DC)(DT) ...String: (DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DT) (DA)(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DC) (DT)(DC)(DT)(DT)(DC)(DT)(DT)(DA) (DG)(DT)(DA)(DT)(DT)(DA)(DC)(DC)(DC)(DC) (DT)(DT) (DC)(DC)(DG)(DG)(DT)(DA)(DG) (DG)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DC) (DA)(DG)(DC) (DG)(DC)(DT)(DT)(DG)(DC) (DG)(DG)(DT)(DC)(DG)(DT)(DT)(DC)(DT)(DG) (DC)(DA)(DT)(DC) (DG)(DG)(DG)(DT)(DC) (DG)(DC)(DG)(DC)(DA)(DG)(DC)(DC)(DG)(DG) (DC)(DG)(DG)(DT)(DA) (DC)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DA)(DT)(DT)(DA)(DC)(DC) (DG)(DG)(DA)(DC)(DG)(DA) (DA)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DT)(DT) |
-Macromolecule #4: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')
Macromolecule | Name: DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 46.29148 KDa |
Sequence | String: (DA)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT) (DT)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC) (DT)(DG)(DC)(DG)(DC)(DG) ...String: (DA)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT) (DT)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC) (DT)(DG)(DC)(DG)(DC)(DG)(DA)(DC) (DC)(DC)(DG)(DA)(DT)(DG)(DC)(DA)(DG)(DA) (DA)(DC) (DG)(DA)(DC)(DC)(DG)(DC)(DA) (DA)(DG)(DC)(DG)(DC)(DT)(DG)(DC)(DG)(DC) (DT)(DC)(DC) (DG)(DA)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DG)(DA)(DA)(DG)(DG)(DG)(DG) (DT)(DA)(DA)(DT) (DA)(DC)(DT)(DA)(DA) (DG)(DA)(DA)(DG)(DA)(DG)(DC)(DG)(DA)(DA) (DG)(DG)(DC)(DC)(DG) (DC)(DC)(DG)(DT) (DA)(DG)(DC)(DC)(DC)(DT)(DA)(DC)(DG)(DG) (DG)(DC)(DG)(DC)(DA)(DA) (DC)(DG)(DT) (DC)(DC)(DG)(DG)(DT)(DA)(DC) |
-Macromolecule #5: 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]eth...
Macromolecule | Name: 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]ethylamino]methyl]-4H-1,4-benzothiazin-3-one type: ligand / ID: 5 / Number of copies: 1 / Formula: A1H5Q |
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Molecular weight | Theoretical: 447.513 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.9 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8s7o: |