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Yorodumi- EMDB-50185: KS + AT di-domain of polyketide synthase 13 in Mycobacterium tube... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50185 | |||||||||
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Title | KS + AT di-domain of polyketide synthase 13 in Mycobacterium tuberculosis | |||||||||
Map data | Final map for Pks13 from M. tuberculosis | |||||||||
Sample |
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Keywords | Mycolic acid synthesis / Claisen condensation / cell wall synthesis / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | Function and homology information DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Johnston HE / Futterer K | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To be published Title: CryoEM structure of the di-domain core of Mycobacterium tuberculosis polyketide synthase 13, essential for mycobacterial mycolic acid synthesis Authors: Johnston HE / Batt SM / Brown AK / Savva CG / Besra GS / Futterer K | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50185.map.gz | 10.2 MB | EMDB map data format | |
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Header (meta data) | emd-50185-v30.xml emd-50185.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_50185.png | 71.1 KB | ||
Filedesc metadata | emd-50185.cif.gz | 6.7 KB | ||
Others | emd_50185_half_map_1.map.gz emd_50185_half_map_2.map.gz | 141.7 MB 141.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50185 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50185 | HTTPS FTP |
-Validation report
Summary document | emd_50185_validation.pdf.gz | 858.4 KB | Display | EMDB validaton report |
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Full document | emd_50185_full_validation.pdf.gz | 858 KB | Display | |
Data in XML | emd_50185_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_50185_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50185 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50185 | HTTPS FTP |
-Related structure data
Related structure data | 9f48MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_50185.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Final map for Pks13 from M. tuberculosis | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map 1
File | emd_50185_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_50185_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Subunit of Pks13
Entire | Name: Subunit of Pks13 |
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Components |
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-Supramolecule #1: Subunit of Pks13
Supramolecule | Name: Subunit of Pks13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) / Strain: H37Rv |
Molecular weight | Theoretical: 187 KDa |
-Macromolecule #1: Polyketide synthase Pks13
Macromolecule | Name: Polyketide synthase Pks13 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 186.642188 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MADVAESQEN APAERAELTV PEMRQWLRNW VGKAVGKAPD SIDESVPMVE LGLSSRDAVA MAADIEDLTG VTLSVAVAFA HPTIESLAT RIIEGEPETD LAGDDAEDWS RTGPAERVDI AIVGLSTRFP GEMNTPEQTW QALLEGRDGI TDLPDGRWSE F LEEPRLAA ...String: MADVAESQEN APAERAELTV PEMRQWLRNW VGKAVGKAPD SIDESVPMVE LGLSSRDAVA MAADIEDLTG VTLSVAVAFA HPTIESLAT RIIEGEPETD LAGDDAEDWS RTGPAERVDI AIVGLSTRFP GEMNTPEQTW QALLEGRDGI TDLPDGRWSE F LEEPRLAA RVAGARTRGG YLKDIKGFDS EFFAVAKTEA DNIDPQQRMA LELTWEALEH ARIPASSLRG QAVGVYIGSS TN DYSFLAV SDPTVAHPYA ITGTSSSIIA NRVSYFYDFH GPSVTIDTAC SSSLVAIHQG VQALRNGEAD VVVAGGVNAL ITP MVTLGF DEIGAVLAPD GRIKSFSADA DGYTRSEGGG MLVLKRVDDA RRDGDAILAV IAGSAVNHDG RSNGLIAPNQ DAQA DVLRR AYKDAGIDPR TVDYIEAHGT GTILGDPIEA EALGRVVGRG RPADRPALLG AVKTNVGHLE SAAGAASMAK VVLAL QHDK LPPSINFAGP SPYIDFDAMR LKMITTPTDW PRYGGYALAG VSSFGFGGAN AHVVVREVLP RDVVEKEPEP EPEPKA AAE PAEAPTLAGH ALRFDEFGNI ITDSAVAEEP EPELPGVTEE ALRLKEAALE ELAAQEVTAP LVPLAVSAFL TSRKKAA AA ELADWMQSPE GQASSLESIG RSLSRRNHGR SRAVVLAHDH DEAIKGLRAV AAGKQAPNVF SVDGPVTTGP VWVLAGFG A QHRKMGKSLY LRNEVFAAWI EKVDALVQDE LGYSVLELIL DDAQDYGIET TQVTIFAIQI ALGELLRHHG AKPAAVIGQ SLGEAASAYF AGGLSLRDAT RAICSRSHLM GEGEAMLFGE YIRLMALVEY SADEIREVFS DFPDLEVCVY AAPTQTVIGG PPEQVDAIL ARAEAEGKFA RKFATKGASH TSQMDPLLGE LTAELQGIKP TSPTCGIFST VHEGRYIKPG GEPIHDVEYW K KGLRHSVY FTHGIRNAVD SGHTTFLELA PNPVALMQVA LTTADAGLHD AQLIPTLARK QDEVSSMVST MAQLYVYGHD LD IRTLFSR ASGPQDYANI PPTRFKRKEH WLPAHFSGDG STYMPGTHVA LPDGRHVWEY APRDGNVDLA ALVRAAAAHV LPD AQLTAA EQRAVPGDGA RLVTTMTRHP GGASVQVHAR IDESFTLVYD ALVSRAGSES VLPTAVGAAT AIAVADGAPV APET PAEDA DAETLSDSLT TRYMPSGMTR WSPDSGETIA ERLGLIVGSA MGYEPEDLPW EVPLIELGLD SLMAVRIKNR VEYDF DLPP IQLTAVRDAN LYNVEKLIEY AVEHRDEVQQ LHEHQKTQTA EEIARAQAEL LHGKVGKTEP VDSEAGVALP SPQNGE QPN PTGPALNVDV PPRDAAERVT FATWAIVTGK SPGGIFNELP RLDDEAAAKI AQRLSERAEG PITAEDVLTS SNIEALA DK VRTYLEAGQI DGFVRTLRAR PEAGGKVPVF VFHPAGGSTV VYEPLLGRLP ADTPMYGFER VEGSIEERAQ QYVPKLIE M QGDGPYVLVG WSLGGVLAYA CAIGLRRLGK DVRFVGLIDA VRAGEEIPQT KEEIRKRWDR YAAFAEKTFN VTIPAIPYE QLEELDDEGQ VRFVLDAVSQ SGVQIPAGII EHQRTSYLDN RAIDTAQIQP YDGHVTLYMA DRYHDDAIMF EPRYAVRQPD GGWGEYVSD LEVVPIGGEH IQAIDEPIIA KVGEHMSRAL GQIEADRTSE VGKQ UniProtKB: Polyketide synthase Pks13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 7.9 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris Details: 20 mM Tris-HCl pH 7.9, 50 mM NaCl, 2.5 mM beta-mercaptoethanol |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1412 / Average exposure time: 3.0 sec. / Average electron dose: 16.5 e/Å2 / Details: movie mode |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |