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- PDB-8p02: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with... -

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Basic information

Entry
Database: PDB / ID: 8p02
TitleCryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA
ComponentsPhthaloyl-CoA decarboxylase (Pcd)
KeywordsFLAVOPROTEIN / prFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase / benzoyl CoA / product bound
Function / homologybenzoyl coenzyme A / hydroxylated prenyl-FMN / : / :
Function and homology information
Biological speciesThauera chlorobenzoica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKayastha, K. / Ermler, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA
Authors: Kayastha, K. / Ermler, U.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 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 (Pcd)
B: Phthaloyl-CoA decarboxylase (Pcd)
C: Phthaloyl-CoA decarboxylase (Pcd)
D: Phthaloyl-CoA decarboxylase (Pcd)
E: Phthaloyl-CoA decarboxylase (Pcd)
F: Phthaloyl-CoA decarboxylase (Pcd)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,72542
Polymers346,0956
Non-polymers9,63036
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area41120 Å2
ΔGint-490 kcal/mol
Surface area88280 Å2
MethodPISA

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Phthaloyl-CoA decarboxylase (Pcd) / UbiD family decarboxylase


Mass: 57682.492 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: Pcd monomers bound with co-factors prFMN, Fe, K and reaction product, Benzoyl-CoA.
Source: (natural) Thauera chlorobenzoica (bacteria)

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Non-polymers , 6 types, 95 molecules

#2: Chemical
ChemComp-BYC / benzoyl coenzyme A


Mass: 871.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C28H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Phthaloyl-CoA decarboxylase (Pcd) bound with benzoyl-CoA
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: 3.38 sec. / Electron dose: 52.27 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6743
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
1crYOLOparticle selection
2EPU2.9.1image acquisition
4Gctf1.06CTF correction
7Coot0.9model fitting
9PHENIX1.14model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2081809
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 821681 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: pdb from the first holo-complex was used / Source name: Other / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0125487
ELECTRON MICROSCOPYf_angle_d0.95634683
ELECTRON MICROSCOPYf_dihedral_angle_d8.98414927
ELECTRON MICROSCOPYf_chiral_restr0.0563684
ELECTRON MICROSCOPYf_plane_restr0.0074457

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