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- PDB-8k0a: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase ... -

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Basic information

Entry
Database: PDB / ID: 8k0a
TitleCryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex
Components
  • 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
  • 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
KeywordsBIOSYNTHETIC PROTEIN / 3-phenylpropionate/cinnamic acid dioxygenase
Function / homology
Function and homology information


3-phenylpropanoate dioxygenase / 3-phenylpropionate dioxygenase activity / 3-phenylpropionate dioxygenase complex / 3-phenylpropionate catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
3-phenylpropionate/cinnamic acid dioxygenase, alpha subunit / 3-phenylpropionate/cinnamic acid dioxygenase, beta subunit / : / : / Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) ...3-phenylpropionate/cinnamic acid dioxygenase, alpha subunit / 3-phenylpropionate/cinnamic acid dioxygenase, beta subunit / : / : / Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily
Similarity search - Domain/homology
3-phenylpropionate/cinnamic acid dioxygenase subunit alpha / 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex
Authors: Jiang, W.X. / Cheng, X.Q. / Wu, M. / Ma, L.X. / Xing, Q.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
B: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
C: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
D: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
E: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
F: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta


Theoretical massNumber of molelcules
Total (without water)215,3266
Polymers215,3266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "A"
d_3ens_1chain "E"
d_1ens_2chain "D"
d_2ens_2chain "F"
d_3ens_2chain "B"

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LYSLYSCC1 - 4531 - 453
d_2ens_1LYSLYSAA1 - 4531 - 453
d_3ens_1LYSLYSEE1 - 4531 - 453
d_1ens_2PHEPHEDD1 - 1721 - 172
d_2ens_2PHEPHEFF1 - 1721 - 172
d_3ens_2PHEPHEBB1 - 1721 - 172

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.500013409176, -0.866017661853, 1.88799150116E-6), (0.866017661825, -0.500013409139, 9.38847389141E-6), (-7.18656314089E-6, 6.32939682278E-6, 0.999999999954)321.78144284, 86.2267104389, -2.48626834889E-5
2given(-0.500017515201, 0.866015291139, -2.34426580397E-6), (-0.866015291117, -0.500017515163, 9.03294499064E-6), (6.65049452374E-6, 6.54680074184E-6, 0.999999999956)86.2285993224, 321.781594889, -0.0014687109586
3given(-0.500009991367, -0.866019635189, -1.02640280434E-6), (0.866019635189, -0.500009991368, 5.86775676288E-7), (-1.02137091445E-6, -5.95491281335E-7, 0.999999999999)321.781571807, 86.2274887472, 0.000201867813189
4given(-0.500011063374, 0.866019016248, 7.67216883869E-8), (-0.866019016248, -0.500011063374, -1.02970501069E-6), (-8.53382427394E-7, -5.81306338461E-7, 0.999999999999)86.2270488048, 321.782328396, 0.000180733286925

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Components

#1: Protein 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha


Mass: 51166.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hcaE, digA, hcaA, hcaA1, phdC1, yfhU, b2538, JW2522
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0ABR5, 3-phenylpropanoate dioxygenase
#2: Protein 3-phenylpropionate/cinnamic acid dioxygenase subunit beta


Mass: 20609.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: hcaF, digB, hcaA2, hcaB, phdC2, yfhV, b2539, JW2523
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q47140, 3-phenylpropanoate dioxygenase

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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: Homohexamer of inositol phosphate phosphatase SopB / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: DIFFRACTION / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30478 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 52.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002815330
ELECTRON MICROSCOPYf_angle_d0.530520799
ELECTRON MICROSCOPYf_chiral_restr0.04462169
ELECTRON MICROSCOPYf_plane_restr0.0042736
ELECTRON MICROSCOPYf_dihedral_angle_d8.62862049
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints0.000596972794935
ens_1d_3CCELECTRON MICROSCOPYNCS constraints0.000640881405119
ens_2d_2DDELECTRON MICROSCOPYNCS constraints0.000577234944625
ens_2d_3DDELECTRON MICROSCOPYNCS constraints0.000581972372805

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