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Yorodumi- EMDB-16632: The ACP crosslinked to the SAT of the cercosporin fungal non-redu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16632 | |||||||||
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Title | The ACP crosslinked to the SAT of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (ACP:SAT-KS-MAT) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Fungal non-reducing polyketide synthase (NR-PKS) / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | Function and homology information secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process Similarity search - Function | |||||||||
Biological species | Cercospora nicotianae (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Munoz-Hernandez H / Tittes YU / Maier T | |||||||||
Funding support | European Union, Switzerland, 2 items
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Citation | Journal: To Be Published Title: CryoEM structure of ACP crosslinked to SAT of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (ACP:SAT-KS-MAT) at 3.4 Angstroms resolution Authors: Munoz-Hernandez H / Maier T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16632.map.gz | 107.9 MB | EMDB map data format | |
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Header (meta data) | emd-16632-v30.xml emd-16632.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_16632.png | 49.4 KB | ||
Filedesc metadata | emd-16632.cif.gz | 6.7 KB | ||
Others | emd_16632_half_map_1.map.gz emd_16632_half_map_2.map.gz | 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16632 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16632 | HTTPS FTP |
-Validation report
Summary document | emd_16632_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16632_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16632_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_16632_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16632 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16632 | HTTPS FTP |
-Related structure data
Related structure data | 8cg6MC 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_16632.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16632_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16632_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ACP crosslinked to the SAT of the starting region of the Non-redu...
Entire | Name: ACP crosslinked to the SAT of the starting region of the Non-reducing polyketide synthase CTB1 -SKM- |
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Components |
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-Supramolecule #1: ACP crosslinked to the SAT of the starting region of the Non-redu...
Supramolecule | Name: ACP crosslinked to the SAT of the starting region of the Non-reducing polyketide synthase CTB1 -SKM- type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Cercospora nicotianae (fungus) |
-Macromolecule #1: Non-reducing polyketide synthase CTB1
Macromolecule | Name: Non-reducing polyketide synthase CTB1 / 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: Cercospora nicotianae (fungus) |
Molecular weight | Theoretical: 140.22 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEDGAQMRVV AFGDQTYDCS EAVSQLLRVR DDAIVVDFLE RAPAVLKAEL ARLSSEQQEE TPRFATLAEL VPRYRAGTLN PAVSQALTC IAQLGLFIRQ HSSGQEAYPT AHDSCITGVC TGALTAVAVG SASSVTALVP LALHTVAVAV RLGARAWEIG S CLADARRG ...String: MEDGAQMRVV AFGDQTYDCS EAVSQLLRVR DDAIVVDFLE RAPAVLKAEL ARLSSEQQEE TPRFATLAEL VPRYRAGTLN PAVSQALTC IAQLGLFIRQ HSSGQEAYPT AHDSCITGVC TGALTAVAVG SASSVTALVP LALHTVAVAV RLGARAWEIG S CLADARRG ANGRYASWTS AVGGISPQDL QDRISAYTAE QALASVSVPY LSAAVGPGQS SVSAAPVILD AFLSTLLRPL TT TRLPITA PYHAPHLFTA KDVQHVTDCL PPSEAWPTVR IPIISFSRDE AVSRGASFPA AMSEAVRDCL IRPIALDRMA VSI ANHARD LGKDSVLPSP IALSFSDKLG PQVNSHLPGA KAPTPELTSK SIPSAIGAEQ QPMAKSPIAI LAASGRFPQS SSMD QFWDV LINGVDTHEL VPPTRWNAAT HVSEDPKAKN VSGTGFGCWL HEAGEFDAAY FNMSPREAPQ VDPAQRLALL TATEA LEQA GVVPNRTSST QKNRVGVWYG ATSNDWMETN SAQNVDTYFI PGGNRAFIPG RVNYFHKFSG PSYTIDTACS SSLAAL HMA CNALWRGEVD TAIVGGTNVL TNPDMTAGLD AGHFLSRSGN CKTFDDEADG YCRGEAVVTL ILKRLPDAQA DKDPIQA SI LGIATNHSAE AASITRPHAG AQQDLFQQVL TETGLTANDI SVCEMAGTGT QAGDSGETTS VVETLAPLNR SGSAVRTT P LYIGAVKSNV GHAESAAGVS SLAKILLMLK HSKIPPHVGI KTKLNHRLPD LAARNTHIAR SEVPWPRPKN GKRRVLLNN FSAAGGNTCL VLEDAPEPED SQEVDPREHH IVALSAKTPD SMVNNLTNMI TWIDKHSGDS LATLPQLSYT TTARRVHHRH RAVATGTDL LQIRSSLQEQ LDRRVSGERS IPHPPNGPSF VLAFTGQGSA FAGMGVDLYK RFASFRSDIA RYDQICEGMS L PSIKAMFE DEKVFSTASP TLQQLTHVCF QMALYRLWKS LGVQAKAVVG HALGEYAALY AAGVLSQSDT LYLVGRRAQL ME KHLSQGT HAMLAVRAKE EAIVAAIDGP PGEAYEFSCR NGEQRNVLGG TVAQIQAAKA ALEAKKIRCQ YLDTPMAFHT GQV DPILPE LLQVAAACSI QDPQIPVISP AYGKVIRSAK DFQPEYFTHH CRSSVNMVDA LQSAVEEGLL DKNVIGLEIG PGPV VTQFV KEAVGTTMQT FASINKDKDT WQLMTQALAK FYLAGASVEW SRYHEDFPGA QKVLELPAYG WALKNYWLQY VNDWS LRKG DPAVVVAASA AALEHHHHHH UniProtKB: Non-reducing polyketide synthase CTB1 |
-Macromolecule #2: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
Macromolecule | Name: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1 type: protein_or_peptide / ID: 2 Details: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1 Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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Source (natural) | Organism: Cercospora nicotianae (fungus) |
Molecular weight | Theoretical: 9.892837 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMDPSPNE IGTVWRDALK ILSEESGLTD EELTDDTSFA DVGVDSLMSL VITSRLRDEL DIDFPDRALF EECQTIFDLR KRFSGSTE UniProtKB: Non-reducing polyketide synthase CTB1 |
-Macromolecule #3: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-...
Macromolecule | Name: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide type: ligand / ID: 3 / Number of copies: 1 / Formula: 42X |
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Molecular weight | Theoretical: 397.361 Da |
Chemical component information | ChemComp-42X: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number grids imaged: 3 / Number real images: 6061 / Average electron dose: 98.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.3000000000000003 µm / Calibrated defocus min: 0.9 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8cg6: |