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Yorodumi- EMDB-33402: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33402 | |||||||||
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Title | Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 (MeFDH1) | |||||||||
Map data | A auto-sharpened cryo EM map of MeFDH1 | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Park J / Heo YY / Roh SH / Lee HH | |||||||||
Funding support | Korea, Republic Of, 2 items
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Citation | Journal: To Be Published Title: Enzymatic conversion of CO2 in real flue gas to molar-scale formate Authors: Jeon BW / Heo YY / Park J / Roh SH / Lee HH / Kim YH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33402.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-33402-v30.xml emd-33402.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33402_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_33402.png | 116.2 KB | ||
Filedesc metadata | emd-33402.cif.gz | 7.4 KB | ||
Others | emd_33402_additional_1.map.gz emd_33402_half_map_1.map.gz emd_33402_half_map_2.map.gz | 49 MB 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33402 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33402 | HTTPS FTP |
-Validation report
Summary document | emd_33402_validation.pdf.gz | 771.9 KB | Display | EMDB validaton report |
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Full document | emd_33402_full_validation.pdf.gz | 771.5 KB | Display | |
Data in XML | emd_33402_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_33402_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33402 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33402 | HTTPS FTP |
-Related structure data
Related structure data | 7xqwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33402.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | A auto-sharpened cryo EM map of MeFDH1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: A density modified map of MeFDH1 from Phenix Resolve EM
File | emd_33402_additional_1.map | ||||||||||||
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Annotation | A density modified map of MeFDH1 from Phenix Resolve EM | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A half map of MeFDH1
File | emd_33402_half_map_1.map | ||||||||||||
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Annotation | A half map of MeFDH1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A half map of MeFDH1
File | emd_33402_half_map_2.map | ||||||||||||
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Annotation | A half map of MeFDH1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ...
+Supramolecule #1: Formate dehydrogenase (FDH) from Methylobacterium extorquens AM1 ...
+Supramolecule #2: Alpha subunit of formate dehydrogenase (FDH) from Methylobacteriu...
+Supramolecule #3: Beta subunit of formate dehydrogenase (FDH) from Methylobacterium...
+Macromolecule #1: Formate dehydrogenase
+Macromolecule #2: Tungsten-containing formate dehydrogenase beta subunit
+Macromolecule #3: TUNGSTEN ION
+Macromolecule #4: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,1...
+Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #6: IRON/SULFUR CLUSTER
+Macromolecule #7: FLAVIN MONONUCLEOTIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds. |
Details | This sample was monodisperse |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1761 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 92000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |