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Yorodumi- EMDB-16004: Structure of hexameric subcomplexes (Truncation Delta2-6) of the ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16004 | ||||||||||||
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Title | Structure of hexameric subcomplexes (Truncation Delta2-6) of the fractal citrate synthase from Synechococcus elongatus PCC7942 | ||||||||||||
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Sample |
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Keywords | Fractal complex / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||||||||
Biological species | Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||||||||
Authors | Lo YK / Bohn S / Sendker FL / Schuller JM / Hochberg G | ||||||||||||
Funding support | Germany, European Union, 3 items
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Citation | Journal: To Be Published Title: Evolution of a protein Sierpinski fractal Authors: Sendker LF / Lo YK / Heimerl T / Bohn S / Pfister P / Mais N / Sadowska W / Peterson L / Benesch JLP / Marklund E / Bange G / Erb TJ / Schuller JM / Hochberg GKA | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16004.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-16004-v30.xml emd-16004.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16004_fsc.xml | 8.8 KB | Display | FSC data file |
Images | emd_16004.png | 180.8 KB | ||
Filedesc metadata | emd-16004.cif.gz | 5.4 KB | ||
Others | emd_16004_half_map_1.map.gz emd_16004_half_map_2.map.gz | 49.9 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16004 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16004 | HTTPS FTP |
-Validation report
Summary document | emd_16004_validation.pdf.gz | 773.4 KB | Display | EMDB validaton report |
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Full document | emd_16004_full_validation.pdf.gz | 773 KB | Display | |
Data in XML | emd_16004_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_16004_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16004 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16004 | HTTPS FTP |
-Related structure data
Related structure data | 8beiMC 8an1C 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_16004.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
File | emd_16004_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16004_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Truncated (Delta 2-6) variant of the citrate synthase from Synech...
Entire | Name: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942 |
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Components |
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-Supramolecule #1: Truncated (Delta 2-6) variant of the citrate synthase from Synech...
Supramolecule | Name: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) |
-Macromolecule #1: Citrate synthase
Macromolecule | Name: Citrate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 / FACHB-805 |
Molecular weight | Theoretical: 43.879867 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MFRPGLEGVP ATLSSISFVD GQRGVLEYRG ISIEQLAQQS SFLETAYLLI WGHLPTQQEL TEFEHEIRYH RRIKFRIRDM MKCFPDSGH PMDALQASAA ALGLFYSRRA LDDPEYIRAA VVRLLAKIPT MVAAFQLIRK GNDPIQPRDE LDYAANFLYM L TEREPDPV ...String: MFRPGLEGVP ATLSSISFVD GQRGVLEYRG ISIEQLAQQS SFLETAYLLI WGHLPTQQEL TEFEHEIRYH RRIKFRIRDM MKCFPDSGH PMDALQASAA ALGLFYSRRA LDDPEYIRAA VVRLLAKIPT MVAAFQLIRK GNDPIQPRDE LDYAANFLYM L TEREPDPV AARIFDICLT LHAEHTINAS TFSAMVTAST LTDPYAVVAS AVGTLAGPLH GGANEEVLDM LEAIGSVENV EP YLDHCIA TKTRIMGFGH RVYKVKDPRA VILQNLAEQL FDIFGHDPYY EIAVAVEKAA AERLSHKGIY PNVDFYSGLV YRK LGIPSD LFTPVFAIAR VAGWLAHWKE QLNENRIFRP TQIYTGSHNL DYTPIADRDL AIESDLEHHH HHH UniProtKB: Citrate synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 29000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |