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Yorodumi- PDB-8bcm: Structure of Synechococcus elongatus PCC 7942 Rubisco recombinant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bcm | |||||||||
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Title | Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli | |||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / Rubisco / Synechococcus / carbon dioxide fixation / recombinant expression | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||
Authors | Ni, T. / Sun, Y. / Liu, L.N. / Zhang, P. | |||||||||
Funding support | United Kingdom, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bcm.cif.gz | 713.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bcm.ent.gz | 594.9 KB | Display | PDB format |
PDBx/mmJSON format | 8bcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bcm_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8bcm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8bcm_validation.xml.gz | 106 KB | Display | |
Data in CIF | 8bcm_validation.cif.gz | 164.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/8bcm ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bcm | HTTPS FTP |
-Related structure data
Related structure data | 15966MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 13349.196 Da / Num. of mol.: 8 / Fragment: Rubisco small subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 / Gene: Synpcc7942_1427 / Production host: Escherichia coli (E. coli) References: UniProt: Q31NB2, ribulose-bisphosphate carboxylase #2: Protein | Mass: 52516.605 Da / Num. of mol.: 8 / Fragment: Rubisco large subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 / Gene: cbbL, rbcL, Synpcc7942_1426 / Production host: Escherichia coli (E. coli) References: UniProt: Q31NB3, ribulose-bisphosphate carboxylase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Synechococcus elongatus PCC 7942 Rubisco recombinantly co-expressed in E.coli Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D4 (2x4 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219865 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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