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Yorodumi- EMDB-15966: Structure of Synechococcus elongatus PCC 7942 Rubisco recombinant... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15966 | |||||||||
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Title | Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | Rubisco / Synechococcus / carbon dioxide fixation / recombinant expression / BIOSYNTHETIC PROTEIN | |||||||||
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 | Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||
Authors | Ni T / Sun Y / Liu LN / Zhang P | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To Be Published Title: Structure of Rubisco Authors: Sun Y / Ni T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15966.map.gz | 93.4 MB | EMDB map data format | |
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Header (meta data) | emd-15966-v30.xml emd-15966.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_15966.png | 117 KB | ||
Filedesc metadata | emd-15966.cif.gz | 5.4 KB | ||
Others | emd_15966_half_map_1.map.gz emd_15966_half_map_2.map.gz | 91.8 MB 91.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15966 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15966 | HTTPS FTP |
-Validation report
Summary document | emd_15966_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_15966_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_15966_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_15966_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15966 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15966 | HTTPS FTP |
-Related structure data
Related structure data | 8bcmMC 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_15966.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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_15966_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_15966_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Synechococcus elongatus PCC 7942 Rubisco recombinantly co-express...
Entire | Name: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli |
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Components |
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-Supramolecule #1: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-express...
Supramolecule | Name: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli 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: Ribulose 1,5-bisphosphate carboxylase small subunit
Macromolecule | Name: Ribulose 1,5-bisphosphate carboxylase small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 |
Molecular weight | Theoretical: 13.349196 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSMKTLPKER RFETFSYLPP LSDRQIAAQI EYMIEQGFHP LIEFNEHSNP EEFYWTMWKL PLFDCKSPQQ VLDEVRECRS EYGDCYIRV AGFDNIKQCQ TVSFIVHRPG RY UniProtKB: Ribulose bisphosphate carboxylase small subunit |
-Macromolecule #2: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 |
Molecular weight | Theoretical: 52.516605 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQG EENSYFAFIA YPLDLFEEGS VTNILTSIVG NVFGFKAIRS LRLEDIRFPV ALVKTFQGPP HGIQVERDLL N KYGRPMLG ...String: MPKTQSAAGY KAGVKDYKLT YYTPDYTPKD TDLLAAFRFS PQPGVPADEA GAAIAAESST GTWTTVWTDL LTDMDRYKGK CYHIEPVQG EENSYFAFIA YPLDLFEEGS VTNILTSIVG NVFGFKAIRS LRLEDIRFPV ALVKTFQGPP HGIQVERDLL N KYGRPMLG CTIKPKLGLS AKNYGRAVYE CLRGGLDFTK DDENINSQPF QRWRDRFLFV ADAIHKSQAE TGEIKGHYLN VT APTCEEM MKRAEFAKEL GMPIIMHDFL TAGFTANTTL AKWCRDNGVL LHIHRAMHAV IDRQRNHGIH FRVLAKCLRL SGG DHLHSG TVVGKLEGDK ASTLGFVDLM REDHIEADRS RGVFFTQDWA SMPGVLPVAS GGIHVWHMPA LVEIFGDDSV LQFG GGTLG HPWGNAPGAT ANRVALEACV QARNEGRDLY REGGDILREA GKWSPELAAA LDLWKEIKFE FETMDKL UniProtKB: Ribulose bisphosphate carboxylase large chain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219865 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8bcm: |