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- EMDB-60635: The CryoEM structure of a C-C bond hydrolase MhpC homotetramer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60635
TitleThe CryoEM structure of a C-C bond hydrolase MhpC homotetramer
Map data
Sample
  • Complex: Homotetramer of a C-C bond hydrolase MhpC
    • Protein or peptide: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
KeywordsC-C bond hydrolase / 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 (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsJiang WX / Cheng XQ / Ma LX / Xing Q
Funding support China, 2 items
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 WX / Cheng XQ / Ma LX / Xing Q
History
DepositionJun 24, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60635.png

Downloads & links

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Map

FileDownload / File: emd_60635.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 360 pix.
= 204.001 Å		0.57 Å/pix.
x 360 pix.
= 204.001 Å		0.57 Å/pix.
x 360 pix.
= 204.001 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.56667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0408
Minimum - Maximum-0.28137338 - 0.33266395
Average (Standard dev.)0.00031617357 (±0.01015749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 204.0012 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60635_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_60635_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 : Homotetramer of a C-C bond hydrolase MhpC

EntireName: Homotetramer of a C-C bond hydrolase MhpC
Components
  • Complex: Homotetramer of a C-C bond hydrolase MhpC
    • Protein or peptide: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase

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Supramolecule #1: Homotetramer of a C-C bond hydrolase MhpC

SupramoleculeName: Homotetramer of a C-C bond hydrolase MhpC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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Macromolecule #1: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hy...

MacromoleculeName: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 31.974436 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSYQPQTEAA TSRFLNVEEA GKTLRIHFND CGQGDETVVL LHGSGPGATG WANFSRNIDP LVEAGYRVIL LDCPGWGKSD SVVNSGSRS DLNARILKSV VDQLDIAKIH LLGNSMGGHS SVAFTLKWPE RVGKLVLMGG GTGGMSLFTP MPTEGIKRLN Q LYRQPTIE ...String:
MSYQPQTEAA TSRFLNVEEA GKTLRIHFND CGQGDETVVL LHGSGPGATG WANFSRNIDP LVEAGYRVIL LDCPGWGKSD SVVNSGSRS DLNARILKSV VDQLDIAKIH LLGNSMGGHS SVAFTLKWPE RVGKLVLMGG GTGGMSLFTP MPTEGIKRLN Q LYRQPTIE NLKLMMDIFV FDTSDLTDAL FEARLNNMLS RRDHLENFVK SLEANPKQFP DFGPRLAEIK AQTLIVWGRN DR FVPMDAG LRLLSGIAGS ELHIFRDCGH WAQWEHADAF NQLVLNFLAR P

UniProtKB: 2-hydroxy-6-oxononadienedioate/2-hydroxy-6-oxononatrienedioate hydrolase

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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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29135
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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