+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15409 | |||||||||
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Title | C1 Cyanobacteria sp PCC 7001 RuBisCO | |||||||||
Map data | Cryo-EM structure of an a-carboxysome RuBisCO enzyme with C1 symmetry at 3.8 A resolution | |||||||||
Sample |
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Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Cyanobium sp. PCC 7001 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.79 Å | |||||||||
Authors | Evans SL / Mann D / Bergeron JRC | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact a-carboxysome Authors: Evans SL / Al-Hazeem MJ / Mann D / Smetacek N / Beavil AJ / Sun Y / Chen T / Dykes GF / Liu L / Bergeron JRC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15409.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-15409-v30.xml emd-15409.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15409_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_15409.png | 59.1 KB | ||
Others | emd_15409_half_map_1.map.gz emd_15409_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15409 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15409 | HTTPS FTP |
-Validation report
Summary document | emd_15409_validation.pdf.gz | 903.6 KB | Display | EMDB validaton report |
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Full document | emd_15409_full_validation.pdf.gz | 903.2 KB | Display | |
Data in XML | emd_15409_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_15409_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15409 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15409 | HTTPS FTP |
-Related structure data
Related structure data | 8cmyM 8aft M: atomic model generated by this map |
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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_15409.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of an a-carboxysome RuBisCO enzyme with C1 symmetry at 3.8 A resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_15409_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15409_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RuBisCO
Entire | Name: RuBisCO |
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Components |
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-Supramolecule #1: RuBisCO
Supramolecule | Name: RuBisCO / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
-Macromolecule #1: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
Molecular weight | Theoretical: 52.526531 KDa |
Sequence | String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF KALRHLRLED IRFPMAFIKT CPGPPNGICV ERDRMNKYGR P LLGCTIKP ...String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF KALRHLRLED IRFPMAFIKT CPGPPNGICV ERDRMNKYGR P LLGCTIKP KLGLSGKNYG RVVYECLRGG LDFTKDDENI NSQPFQRWQN RFEFVAEAVA LAQQETGEKK GHYLNCTAAT PE EMYERAE FAKELGQPII MHDYITGGFT ANTGLSKWCR KNGMLLHIHR AMHAVIDRHP KHGIHFRVLA KCLRLSGGDQ LHT GTVVGK LEGDRQTTLG FIDQLRESFI PEDRSRGNFF DQDWGSMPGV FAVASGGIHV WHMPALVAIF GDDSVLQFGG GTHG HPWGS AAGAAANRVA LEACVKARNA GREIEKESRD ILMEAAKHSP ELAIALETWK EIKFEFDTVD KLDVQ |
-Macromolecule #2: Ribulose bisphosphate carboxylase, small subunit
Macromolecule | Name: Ribulose bisphosphate carboxylase, small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
Molecular weight | Theoretical: 12.880533 KDa |
Sequence | String: MPFKTVGDYQ TVATLETFGF LPPMTQDEIY DQIAYIIAQG WSPLIEHVHP SRSMATYWSY WKLPFFGEKD LGVIVSELEA CHRAYPDHH VRLVGYDAYT QSQGACFVVF EGR |
-Macromolecule #3: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Macromolecule | Name: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: CAP |
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Molecular weight | Theoretical: 356.115 Da |
Chemical component information | ChemComp-CAP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 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: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |