[English] 日本語
Yorodumi
- EMDB-36758: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36758
TitleCryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex
Map data
Sample
  • Complex: Homohexamer of inositol phosphate phosphatase SopB
    • Protein or peptide: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
  • Protein or peptide: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
Keywords3-phenylpropionate/cinnamic acid dioxygenase / BIOSYNTHETIC PROTEIN
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) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. ...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] iron-sulphur domain / Rieske [2Fe-2S] 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 (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex
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

-
Structure visualization

Supplemental images

emd_36758.png

Downloads & links

-
Map

FileDownload / File: emd_36758.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.425 Å
Density
Contour LevelBy AUTHOR: 0.0434
Minimum - Maximum-0.040537566 - 0.122786164
Average (Standard dev.)0.000025314639 (±0.0034459357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_36758_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36758_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
  • Protein or peptide: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta

-
Supramolecule #1: Homohexamer of inositol phosphate phosphatase SopB

SupramoleculeName: Homohexamer of inositol phosphate phosphatase SopB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)

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

MacromoleculeName: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: 3-phenylpropanoate dioxygenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 51.166047 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTTPSDLNIY QLIDTQNGRV TPRIYTDPDI YQLELERIFG RCWLFLAHES QIPKPGDFFN TYMGEDAVVV VRQKDGSIKA FLNQCRHRA MRVSYADCGN TRAFTCPYHG WSYGINGELI DVPLEPRAYP QGLCKSHWGL NEVPCVESYK GLIFGNWDTS A PGLRDYLG ...String:
MTTPSDLNIY QLIDTQNGRV TPRIYTDPDI YQLELERIFG RCWLFLAHES QIPKPGDFFN TYMGEDAVVV VRQKDGSIKA FLNQCRHRA MRVSYADCGN TRAFTCPYHG WSYGINGELI DVPLEPRAYP QGLCKSHWGL NEVPCVESYK GLIFGNWDTS A PGLRDYLG DIAWYLDGML DRREGGTEIV GGVQKWVINC NWKFPAEQFA SDQYHALFSH ASAVQVLGAK DDGSDKRLGD GQ TARPVWE TAKDALQFGQ DGHGSGFFFT EKPDANVWVD GAVSSYYRET YAEAEQRLGE VRALRLAGHN NIFPTLSWLN GTA TLRVWH PRGPDQVEVW AFCITDKAAS DEVKAAFENS ATRAFGPAGF LEQDDSENWC EIQKLLKGHR ARNSKLCLEM GLGQ EKRRD DGIPGITNYI FSETAARGMY QRWADLLSSE SWQEVLDKTA AYQQEVMK

UniProtKB: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha

-
Macromolecule #2: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta

MacromoleculeName: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: 3-phenylpropanoate dioxygenase
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 20.609248 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSAQVSLELH HRISQFLFHE ASLLDDWKFR DWLAQLDEEI RYTMRTTVNA QTRDRRKGVQ PPTTWIFNDT KDQLERRIAR LETGMAWAE EPPSRTRHLI SNCQISETDI PNVFAVRVNY LLYRAQKERD ETFYVGTRFD KVRRLEDDNW RLLERDIVLD Q AVITSHNL SVLF

UniProtKB: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30478
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more