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Yorodumi- PDB-8pmk: Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pmk | ||||||
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Title | Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) complex with prFMN bound | ||||||
Components | Phthaloyl-CoA decarboxylase | ||||||
Keywords | FLAVOPROTEIN / prFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase | ||||||
Function / homology | Function and homology information ferulate metabolic process / cinnamic acid catabolic process / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Thauera chlorobenzoica (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.43 Å | ||||||
Authors | Kayastha, K. / Ermler, U. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Active Pcd complex with prFMN bound Authors: Kayastha, K. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pmk.cif.gz | 583.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pmk.ent.gz | 481 KB | Display | PDB format |
PDBx/mmJSON format | 8pmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pmk_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8pmk_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8pmk_validation.xml.gz | 86.5 KB | Display | |
Data in CIF | 8pmk_validation.cif.gz | 129.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/8pmk ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pmk | HTTPS FTP |
-Related structure data
Related structure data | 17762MC 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: 58985.941 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: prFMN / Source: (gene. exp.) Thauera chlorobenzoica (bacteria) / Gene: Tchl_3080 / Production host: Thauera chlorobenzoica (bacteria) / References: UniProt: A0A193DUB4 #2: Chemical | ChemComp-BYN / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-K / 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 | Name: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.36 MDa / Experimental value: YES |
Source (natural) | Organism: Thauera chlorobenzoica (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.82 sec. / Electron dose: 50.76 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9974 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2206933 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 743306 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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