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Yorodumi- PDB-7xqw: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xqw | |||||||||
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Title | Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1) | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / oxidoreductase | |||||||||
Function / homology | Function and homology information formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding ...formate dehydrogenase / formate metabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase complex / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Methylorubrum extorquens AM1 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Park, J. / Heo, Y.Y. / Roh, S.H. / Lee, H.H. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: To Be Published Title: Enzymatic conversion of CO2 in real flue gas to molar-scale formate Authors: Jeon, B.W. / Heo, Y.Y. / Park, J. / Roh, S.H. / Lee, H.H. / Kim, Y.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xqw.cif.gz | 248.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xqw.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xqw_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7xqw_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7xqw_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 7xqw_validation.cif.gz | 78.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xqw ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xqw | HTTPS FTP |
-Related structure data
Related structure data | 33402MC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 108292.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria) Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: fdh1A, MexAM1_META1p5032 / Production host: Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5ATT7, formate dehydrogenase |
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#2: Protein | Mass: 62397.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylorubrum extorquens AM1 (bacteria) Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: fdh1B, MexAM1_META1p5031 / Production host: Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5ATT6, formate dehydrogenase |
-Non-polymers , 5 types, 10 molecules
#3: Chemical | ChemComp-W / | ||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SF4 / #7: Chemical | ChemComp-FMN / | |
-Details
Has ligand of interest | Y |
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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 |
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Molecular weight | Value: 0.16 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | ||||||||||||||||||||||||
Specimen support | 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: 285 K / Details: blot for 3 seconds |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1761 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2188878 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 453262 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 136.6 / Protocol: RIGID BODY FIT / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7E5Z Accession code: 7E5Z / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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