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- PDB-8pmk: Cryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) com... -

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Basic information

Entry
Database: PDB / ID: 8pmk
TitleCryo-EM structure of active Phthaloyl-CoA decarboxylase (Pcd) complex with prFMN bound
ComponentsPhthaloyl-CoA decarboxylase
KeywordsFLAVOPROTEIN / 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
: / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
hydroxylated prenyl-FMN / : / : / Phthaloyl-CoA decarboxylase
Similarity search - Component
Biological speciesThauera chlorobenzoica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsKayastha, K. / Ermler, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Active Pcd complex with prFMN bound
Authors: Kayastha, K. / Ermler, U.
History
DepositionJun 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phthaloyl-CoA decarboxylase
B: Phthaloyl-CoA decarboxylase
C: Phthaloyl-CoA decarboxylase
D: Phthaloyl-CoA decarboxylase
E: Phthaloyl-CoA decarboxylase
F: Phthaloyl-CoA decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,41036
Polymers353,9166
Non-polymers4,49530
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40090 Å2
ΔGint-439 kcal/mol
Surface area90130 Å2

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Components

#1: Protein
Phthaloyl-CoA decarboxylase


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 / hydroxylated prenyl-FMN


Mass: 542.476 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H31N4O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Active Phthaloyl-CoA decarboxylase with prFMN co-factor bound
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.36 MDa / Experimental value: YES
Source (natural)Organism: Thauera chlorobenzoica (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPU2.9.1image acquisition
4Gctf1.06CTF correction
7Coot0.9model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2206933
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 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 buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00724540
ELECTRON MICROSCOPYf_angle_d1.09633360
ELECTRON MICROSCOPYf_dihedral_angle_d9.7383324
ELECTRON MICROSCOPYf_chiral_restr0.0593570
ELECTRON MICROSCOPYf_plane_restr0.0094332

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