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- PDB-8oz5: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8oz5 | ||||||
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Title | Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with substrate analog/inhibitor, 2-CN-benzoyl-CoA | ||||||
![]() | Phthaloyl-CoA decarboxylase (Pcd) | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | hydroxylated prenyl-FMN / : / : / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 545.1 KB | Display | ![]() |
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PDB format | ![]() | 456.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 17298MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 57682.492 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 6 types, 148 molecules ![](data/chem/img/BYN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BYN / #3: Chemical | ChemComp-WC8 / Mass: 896.650 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H39N8O17P3S / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-FE / ![]() #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.36 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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 |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.65 sec. / Electron dose: 50.08 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6250 |
EM imaging optics | Energyfilter name![]() |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2071338 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 675429 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: pdb from the first holo-complex was used / Source name: Other / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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