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- EMDB-17762: Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) com... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) complex with prFMN bound | |||||||||
![]() | PCD holo-complex with prFMN co-factor bound | |||||||||
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![]() | prFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase / FLAVOPROTEIN | |||||||||
Function / homology | ![]() 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||
![]() | Kayastha K / Ermler U | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Active Pcd complex with prFMN bound Authors: Kayastha K / Ermler U | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 40.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 153.1 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 40.5 MB 40.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 698.7 KB | Display | ![]() |
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Full document | ![]() | 698.3 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pmkMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | PCD holo-complex with prFMN co-factor bound | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.116 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17762_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17762_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
Entire | Name: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound |
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Components |
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-Supramolecule #1: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
Supramolecule | Name: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 360 KDa |
-Macromolecule #1: Phthaloyl-CoA decarboxylase
Macromolecule | Name: Phthaloyl-CoA decarboxylase / type: protein_or_peptide / ID: 1 / Details: prFMN / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.985941 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MNDLATKGIS EAAERVGEKD LRAALEWFRS KGYLVETNKE VNPDLEITGL QKIFDGSLPM LFNNVKDMPH ARAITNLFGD IRVVEELFG WENSLDRVKK VARAIDHPLK PVIIGQDEAP VQEEVLTTDL DVNKWLTAIR HTPLETEMTI GSGISCVVGP Y FDGGSHIG ...String: MNDLATKGIS EAAERVGEKD LRAALEWFRS KGYLVETNKE VNPDLEITGL QKIFDGSLPM LFNNVKDMPH ARAITNLFGD IRVVEELFG WENSLDRVKK VARAIDHPLK PVIIGQDEAP VQEEVLTTDL DVNKWLTAIR HTPLETEMTI GSGISCVVGP Y FDGGSHIG YNRMNFRWGN VGTFQISPGS HMWQVMTEHY KDDEPIPLTM CFGVPPSCTY VAGAGFDYAI LPKGCDEIGI AG AIQGSPV RLVKCRTIDA YTLADAEYVL EGYLHPRDKR YETAESEAAD IQGRFHFHPE WAGYMGKAYK APTFHVTAIT MRR RESKPI IFPLGVHTAD DANIDTSVRE SAIFALCERL QPGIVQNVHI PYCMTDWGGC IIQVKKRNQI EEGWQRNFLA AILA CSQGM RLAIAVSEDV DIYSMDDIMW CLTTRVNPQT DILNPLPGGR GQTFMPAERM TSGDKQWTAS NTQFEGGMGI DATVP YGYE SDFHRPVYGV DLVKPENFFD AKDIDKMKSR MAGWVLSLAR TGR UniProtKB: Phthaloyl-CoA decarboxylase |
-Macromolecule #2: hydroxylated prenyl-FMN
Macromolecule | Name: hydroxylated prenyl-FMN / type: ligand / ID: 2 / Number of copies: 6 / Formula: BYN |
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Molecular weight | Theoretical: 542.476 Da |
Chemical component information | ![]() ChemComp-BYN: |
-Macromolecule #3: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 3 / Number of copies: 18 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #4: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 135 sec. / Pretreatment - Pressure: 38.0 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9974 / Average exposure time: 2.82 sec. / Average electron dose: 50.76 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8pmk: |