[English] 日本語
Yorodumi- PDB-8bei: Structure of hexameric subcomplexes (Truncation Delta2-6) of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bei | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of hexameric subcomplexes (Truncation Delta2-6) of the fractal citrate synthase from Synechococcus elongatus PCC7942 | ||||||||||||
Components | Citrate synthase | ||||||||||||
Keywords | TRANSFERASE / Fractal complex | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||||||||
Authors | Lo, Y.K. / Bohn, S. / Sendker, F.L. / Schuller, J.M. / Hochberg, G. | ||||||||||||
Funding support | Germany, European Union, 3items
| ||||||||||||
Citation | Journal: To Be Published Title: Evolution of a protein Sierpinski fractal Authors: Sendker, L.F. / Lo, Y.K. / Heimerl, T. / Bohn, S. / Pfister, P. / Mais, N. / Sadowska, W. / Peterson, L. / Benesch, J.L.P. / Marklund, E. / Bange, G. / Erb, T.J. / Schuller, J.M. / Hochberg, G.K.A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bei.cif.gz | 396.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bei.ent.gz | 327.9 KB | Display | PDB format |
PDBx/mmJSON format | 8bei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8bei ftp://data.pdbj.org/pub/pdb/validation_reports/be/8bei | HTTPS FTP |
---|
-Related structure data
Related structure data | 16004MC 8an1C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 43879.867 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 / FACHB-805 / Gene: Synpcc7942_0612 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31QM5 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Truncated (Delta 2-6) variant of the citrate synthase from Synechococcus elongatus PCC7942 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 774026 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|