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Yorodumi- PDB-8xcz: Cryo-EM structure of glutamate dehydrogenase from thermococcus pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xcz | |||||||||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus incorporating NADP and GLU in the steady 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: 2.83 Å | |||||||||||||||||||||||||||||||||||||||||||||
Authors | Wakabayashi, T. / Oide, M. / Nakasako, M. | |||||||||||||||||||||||||||||||||||||||||||||
Funding support | Japan, 14items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xcz.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xcz.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 8xcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/8xcz ftp://data.pdbj.org/pub/pdb/validation_reports/xc/8xcz | HTTPS FTP |
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-Related structure data
Related structure data | 38260MC 8xcoC 8xcpC 8xcqC 8xcrC 8xcsC 8xctC 8xcuC 8xcvC 8xcwC 8xcxC 8xcyC 8xd0C 8xd1C 8xd2C 8xd3C 8xd4C 8xd5C 8xd6C 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: 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)+] |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-GGL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: Hexamer of glutamate dehydrogenase in the presence of NADP and glutamate Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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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 |
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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 room temperature was flash-frozen 1-h after mixing GDH, NADP and glutamate solutions. |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 Details: Grid information as following: Company/model: Quantifoil Cu 1.2/1.3 Material:Cu Grid mesh: 200 |
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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: 7075 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6334528 Details: Auto-picking based on templates from manually picked GDH particles. | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168650 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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