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- PDB-9ijk: The CryoEM structure of a C-C bond hydrolase MhpC homotetramer -

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Basic information

Entry
Database: PDB / ID: 9ijk
TitleThe CryoEM structure of a C-C bond hydrolase MhpC homotetramer
Components2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
KeywordsHYDROLASE / C-C bond hydrolase
Function / homology
Function and homology information


2-hydroxy-6-oxonona-2,4-dienedioate hydrolase / 2-hydroxy-6-oxonona-2,4,7-trienedioate hydrolase activity / 3-(3-hydroxy)phenylpropionate catabolic process / 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity / 3-phenylpropionate catabolic process / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
National Science Foundation (NSF, China)32371277 China
CitationJournal: To Be Published
Title: The CryoEM structure of a C-C bond hydrolase MhpC homotetramer
Authors: Jiang, W.X. / Cheng, X.Q. / Ma, L.X. / Xing, Q.
History
DepositionJun 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
B: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
C: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
D: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase


Theoretical massNumber of molelcules
Total (without water)127,8984
Polymers127,8984
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase / 2-hydroxy-6-ketonona-2 / 4-diene-1 / 9-dioic acid 5 / 6-hydrolase / 2-hydroxy-6-oxonona-2 / 4 / 7-triene-1


Mass: 31974.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mhpC, b0349, JW0340
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P77044, 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase
Has protein modificationN

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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: Homotetramer of a C-C bond hydrolase MhpC / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7
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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 33 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: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29135 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 102.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00449192
ELECTRON MICROSCOPYf_angle_d0.625512444
ELECTRON MICROSCOPYf_chiral_restr0.04111356
ELECTRON MICROSCOPYf_plane_restr0.00461636
ELECTRON MICROSCOPYf_dihedral_angle_d4.90711236

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