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- EMDB-36757: CryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase Mh... -

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Basic information

Entry
Database: EMDB / ID: EMD-36757
TitleCryoEM structure of a 2,3-hydroxycinnamic acid 1,2-dioxygenase MhpB in apo form
Map data
Sample
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
Keywordsdioxygenase / BIOSYNTHETIC PROTEIN
Function / homology3-carboxyethylcatechol 2,3-dioxygenase / 3-carboxyethylcatechol 2,3-dioxygenase activity / 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / 3-phenylpropionate catabolic process / ferrous iron binding / 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsJiang WX / Cheng XQ / Ma LX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
CitationJournal: To Be Published
Title: CryoEM structure of the NADP-dependent malic enzyme in complex with oxaloacetate
Authors: Jiang WX / Cheng XQ / Wu M / Ma LX / Xing Q
History
DepositionJul 7, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_36757.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.56667 Å
Density
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.04420653 - 0.14373596
Average (Standard dev.)0.0002270471 (±0.007908443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 226.668 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Homohexamer of inositol phosphate phosphatase SopB

EntireName: Homohexamer of inositol phosphate phosphatase SopB
Components
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase

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Supramolecule #1: Homohexamer of inositol phosphate phosphatase SopB

SupramoleculeName: Homohexamer of inositol phosphate phosphatase SopB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-diox...

MacromoleculeName: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase
type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: 3-carboxyethylcatechol 2,3-dioxygenase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 34.230961 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MHAYLHCLSH SPLVGYVDPA QEVLDEVNGV IASARERIAA FSPELVVLFA PDHYNGFFYD VMPPFCLGVG ATAIGDFGSA AGELPVPVE LAEACAHAVM KSGIDLAVSY CMQVDHGFAQ PLEFLLGGLD KVPVLPVFIN GVATPLPGFQ RTRMLGEAIG R FTSTLNKR ...String:
MHAYLHCLSH SPLVGYVDPA QEVLDEVNGV IASARERIAA FSPELVVLFA PDHYNGFFYD VMPPFCLGVG ATAIGDFGSA AGELPVPVE LAEACAHAVM KSGIDLAVSY CMQVDHGFAQ PLEFLLGGLD KVPVLPVFIN GVATPLPGFQ RTRMLGEAIG R FTSTLNKR VLFLGSGGLS HQPPVPELAK ADAHMRDRLL GSGKDLPASE RELRQQRVIS AAEKFVEDQR TLHPLNPIWD NQ FMTLLEQ GRIQELDAVS NEELSAIAGK STHEIKTWVA AFAAISAFGN WRSEGRYYRP IPEWIAGFGS LSARTEN

UniProtKB: 2,3-dihydroxyphenylpropionate/2,3-dihydroxicinnamic acid 1,2-dioxygenase

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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: 7.2
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: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 364814
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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