[English] 日本語
![](img/lk-miru.gif)
- PDB-8znd: Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Th... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8znd | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of W89F mutated Glutamate dehydrogenase from Thermococcus profundus incorporating NADPH and a substrate in the steady stage of reaction | ||||||||||||||||||||||||||||||||||||||||||
![]() | Glutamate dehydrogenase | ||||||||||||||||||||||||||||||||||||||||||
![]() | OXIDOREDUCTASE / Complex / NADPH / substrate / Mutant | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||||||||||||||||||||||||||||||||||||||
![]() | Wakabayashi, T. / Nakasako, M. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||||||||||||||||||||||||||
![]() | ![]() Title: Mechanism for drastic reduction in catalytic activity of Trp89Phe-mutated glutamate dehydrogenase revealed by crystal structure and cryoEM-sampling of metastable conformation in action Authors: Wakabayashi, T. / Oide, M. / Matsui, Y. / Nakasako, M. | ||||||||||||||||||||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 85.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.2 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 60268MC ![]() 8znbC ![]() 8zncC ![]() 8zngC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 46360.004 Da / Num. of mol.: 1 / Mutation: W89F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O74024, glutamate dehydrogenase [NAD(P)+] |
---|---|
#2: Chemical | ChemComp-NDP / |
#3: 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 W89F mutated glutamate dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.280 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 0.5 mM NADP, 100 mM Glutamate in 5 mM Tris-HCl at pH7.5. | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 8.96 mg/mL GDH W89F | ||||||||||||||||||||
Specimen support | Details: Both sides of the grid were glow-discharged for 45 s at 20 mA and 20 Pa. Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K Details: The sample solution was flash-frozen 2-h after mixing the protein solution and buffer solution. |
-
Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 350 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7651 |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3534400 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225530 / Num. of class averages: 1 / Symmetry type: POINT |