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- EMDB-17298: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with... -
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Open data
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Basic information
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Title | Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with substrate analog/inhibitor, 2-CN-benzoyl-CoA | |||||||||
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![]() | prFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase / cyano-benzoyl CoA / inhibitor bound / substrate analog / FLAVOPROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.04 Å | |||||||||
![]() | Kayastha K / Ermler U | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with substrate analog/inhibitor, 2-CN-benzoyl-CoA Authors: Kayastha K / Ermler U | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.5 KB 18.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.5 KB | Display | ![]() |
Images | ![]() | 163.6 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 98.1 MB 98.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 743 KB | Display | ![]() |
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Full document | ![]() | 742.5 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_17298_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17298_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA
Entire | Name: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA |
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Components |
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-Supramolecule #1: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA
Supramolecule | Name: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA 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 (Pcd)
Macromolecule | Name: Phthaloyl-CoA decarboxylase (Pcd) / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 57.682492 KDa |
Sequence | String: ERVGEKDLRA ALEWFRSKGY LVETNKEVNP DLEITGLQKI FDGSLPMLFN NVKDMPHARA ITNLFGDIRV VEELFGWENS LDRVKKVAR AIDHPLKPVI IGQDEAPVQE EVLTTDLDVN KWLTAIRHTP LETEMTIGSG ISCVVGPYFD GGSHIGYNRM N FRWGNVGT ...String: ERVGEKDLRA ALEWFRSKGY LVETNKEVNP DLEITGLQKI FDGSLPMLFN NVKDMPHARA ITNLFGDIRV VEELFGWENS LDRVKKVAR AIDHPLKPVI IGQDEAPVQE EVLTTDLDVN KWLTAIRHTP LETEMTIGSG ISCVVGPYFD GGSHIGYNRM N FRWGNVGT FQISPGSHMW QVMTEHYKDD EPIPLTMCFG VPPSCTYVAG AGFDYAILPK GCDEIGIAGA IQGSPVRLVK CR TIDAYTL ADAEYVLEGY LHPRDKRYET AESEAADIQG RFHFHPEWAG YMGKAYKAPT FHVTAITMRR RESKPIIFPL GVH TADDAN IDTSVRESAI FALCERLQPG IVQNVHIPYC MTDWGGCIIQ VKKRNQIEEG WQRNFLAAIL ACSQGMRLAI AVSE DVDIY SMDDIMWCLT TRVNPQTDIL NPLPGGRGQT FMPAERMTSG DKQWTASNTQ FEGGMGIDAT VPYGYESDFH RPVYG VDLV KPENFFDAKD IDKMKSRMAG WVLSLARTGR |
-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: 2-CN-benzoyl coenzyme A
Macromolecule | Name: 2-CN-benzoyl coenzyme A / type: ligand / ID: 3 / Number of copies: 6 / Formula: WC8 |
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Molecular weight | Theoretical: 896.65 Da |
-Macromolecule #4: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #5: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 112 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-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. |
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: 6250 / Average exposure time: 2.65 sec. / Average electron dose: 50.08 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
Initial model | Chain - Source name: Other / Chain - Initial model type: experimental model / Details: pdb from the first holo-complex was used |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8oz5: |