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- EMDB-17298: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with... -

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Basic information

Entry
Database: EMDB / ID: EMD-17298
TitleCryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with substrate analog/inhibitor, 2-CN-benzoyl-CoA
Map data
Sample
  • Complex: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA
    • Protein or peptide: Phthaloyl-CoA decarboxylase (Pcd)
  • Ligand: hydroxylated prenyl-FMN
  • Ligand: 2-CN-benzoyl coenzyme A
  • Ligand: FE (III) ION
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsprFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase / cyano-benzoyl CoA / inhibitor bound / substrate analog / FLAVOPROTEIN
Biological speciesThauera chlorobenzoica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.04 Å
AuthorsKayastha K / Ermler U
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with substrate analog/inhibitor, 2-CN-benzoyl-CoA
Authors: Kayastha K / Ermler U
History
DepositionMay 8, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17298.png

Downloads & links

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Map

FileDownload / File: emd_17298.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 267.84 Å		0.84 Å/pix.
x 320 pix.
= 267.84 Å		0.84 Å/pix.
x 320 pix.
= 267.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00737
Minimum - Maximum-0.018860474 - 0.07931579
Average (Standard dev.)0.00006756555 (±0.0022237964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17298_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17298_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA

EntireName: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA
Components
  • Complex: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA
    • Protein or peptide: Phthaloyl-CoA decarboxylase (Pcd)
  • Ligand: hydroxylated prenyl-FMN
  • Ligand: 2-CN-benzoyl coenzyme A
  • Ligand: FE (III) ION
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA

SupramoleculeName: Phthaloyl-CoA decarboxylase (Pcd) bound with 2-CN-benzoyl-CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thauera chlorobenzoica (bacteria)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Phthaloyl-CoA decarboxylase (Pcd)

MacromoleculeName: Phthaloyl-CoA decarboxylase (Pcd) / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thauera chlorobenzoica (bacteria)
Molecular weightTheoretical: 57.682492 KDa
SequenceString: 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

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Macromolecule #2: hydroxylated prenyl-FMN

MacromoleculeName: hydroxylated prenyl-FMN / type: ligand / ID: 2 / Number of copies: 6 / Formula: BYN
Molecular weightTheoretical: 542.476 Da
Chemical component information

ChemComp-BYN:
hydroxylated prenyl-FMN

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Macromolecule #3: 2-CN-benzoyl coenzyme A

MacromoleculeName: 2-CN-benzoyl coenzyme A / type: ligand / ID: 3 / Number of copies: 6 / Formula: WC8
Molecular weightTheoretical: 896.65 Da

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Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 112 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: 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.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen 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

Particle selectionNumber selected: 2071338
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 675429
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: pdb from the first holo-complex was used
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8oz5:
Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with substrate analog/inhibitor, 2-CN-benzoyl-CoA

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