[English] 日本語
Yorodumi- PDB-8xcq: Cryo-EM structure of Glutamate dehydrogenase from Thermococcus pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xcq | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Glutamate dehydrogenase from Thermococcus profundus incorporating NADP and GLU in the initial stage of reaction | |||||||||||||||||||||||||||||||||||||||||||||
Components | Glutamate dehydrogenase | |||||||||||||||||||||||||||||||||||||||||||||
Keywords | OXIDOREDUCTASE / Complex / Coenzyme / NADP+ / Glutamate | |||||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process Similarity search - Function | |||||||||||||||||||||||||||||||||||||||||||||
Biological species | Thermococcus profundus (archaea) | |||||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||||||||||||||||||||||||||||||||||||||
Authors | Wakabayashi, T. / Oide, M. / Nakasako, M. | |||||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 14items
| |||||||||||||||||||||||||||||||||||||||||||||
Citation | Journal: To Be Published Title: CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase Authors: Wakabayashi, T. / Oide, M. / Nakasako, M. | |||||||||||||||||||||||||||||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xcq.cif.gz | 86 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xcq.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 8xcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/8xcq ftp://data.pdbj.org/pub/pdb/validation_reports/xc/8xcq | HTTPS FTP |
---|
-Related structure data
Related structure data | 38251MC 8xcoC 8xcpC 8xcrC 8xcsC 8xctC 8xcuC 8xcvC 8xcwC 8xcxC 8xcyC 8xczC 8xd0C 8xd1C 8xd2C 8xd3C 8xd4C 8xd5C 8xd6C 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: 46758.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus profundus (archaea) / Gene: gdhA / Production host: Escherichia coli (E. coli) References: UniProt: O74024, glutamate dehydrogenase [NAD(P)+] | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hexamer of glutamate dehydrogenase in the presence of NADP and glutamate Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.280 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Thermococcus profundus (archaea) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 4.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K Details: The sample solution kept at 277 K was flash-frozen 15-s after mixing GDH, NADP and glutamate solutions. |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 47000 nm / Nominal defocus min: 400 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7750 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5267415 / Details: auto-picking with LoG-fiter inplemented in Relion | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208647 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |