[English] 日本語
Yorodumi
- EMDB-42391: Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild typ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42391
TitleMicrobacterium testaceum C-glucosyl deglycosidase (CGD), wild type (cryo-EM)
Map datarefinement map
Sample
  • Complex: C-glucosyl deglycosidase from Microbacterium testaceum
    • Protein or peptide: Sugar phosphate isomerase
  • Ligand: MANGANESE (II) ION
Keywordsbacterial C-glucosyl deglycosidase / C-C bond cleavage / C-glucosyl flavonoids / Microbacterium tetsaceum NS220 / plant endosymbiont / N-terminal DUF6379 beta-sandwich domain / C-terminal TIM-barrel domain / homodimer / LYASE
Function / homologyDomain of unknown function DUF6379 / C-glycoside deglycosidase beta subunit / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / lyase activity / C-deglycosylation enzyme beta subunit
Function and homology information
Biological speciesMicrobacterium testaceum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsFurlanetto V / Kalyani DC / Hallberg BM / Divne C
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Other governmentFormas 2017-00983 Sweden
Other governmentVR 2017-03877 Sweden
Other privateOscar and Lili Lamm Memorial Foundation DO2017-0020 Sweden
CitationJournal: To be published
Title: Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type (cryo-EM)
Authors: Furlanetto V / Kalyani DC / Srivastava V / Hallberg BM / Ezcurra I / Divne C
History
DepositionOct 18, 2023-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42391.png

Downloads & links

-
Map

FileDownload / File: emd_42391.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 220 pix.
= 223.344 Å		1.02 Å/pix.
x 220 pix.
= 223.344 Å		1.02 Å/pix.
x 220 pix.
= 223.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0152 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.048668887 - 1.5150393
Average (Standard dev.)0.0012761841 (±0.024890034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 223.34401 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: halfmap A

Fileemd_42391_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfmap B

Fileemd_42391_half_map_2.map
Annotationhalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C-glucosyl deglycosidase from Microbacterium testaceum

EntireName: C-glucosyl deglycosidase from Microbacterium testaceum
Components
  • Complex: C-glucosyl deglycosidase from Microbacterium testaceum
    • Protein or peptide: Sugar phosphate isomerase
  • Ligand: MANGANESE (II) ION

-
Supramolecule #1: C-glucosyl deglycosidase from Microbacterium testaceum

SupramoleculeName: C-glucosyl deglycosidase from Microbacterium testaceum
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: wild type
Source (natural)Organism: Microbacterium testaceum (bacteria) / Strain: NS220

-
Macromolecule #1: Sugar phosphate isomerase

MacromoleculeName: Sugar phosphate isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Microbacterium testaceum (bacteria) / Strain: NS220
Molecular weightTheoretical: 48.768133 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MLLERDLIQS VGFRNVREGG EITGFQFRVR MPSYRGMAAS LIDGIGVRIP GLVDVGPDVP LWTLQGQQYT LAELWDGDGV RWPLEDAAI IFVPLPGGLP DGVHELSIEL RLRMSYIPQE HQPSTYRVTK HVTLAPEASG APFRYGVSLY SYMSDYGTVM D LETAMASI ...String:
MLLERDLIQS VGFRNVREGG EITGFQFRVR MPSYRGMAAS LIDGIGVRIP GLVDVGPDVP LWTLQGQQYT LAELWDGDGV RWPLEDAAI IFVPLPGGLP DGVHELSIEL RLRMSYIPQE HQPSTYRVTK HVTLAPEASG APFRYGVSLY SYMSDYGTVM D LETAMASI ADLGATGIEI LGEAHVPNYP NPSDEWVEQW FALLSTYGLE PTNMGSWIDT RLHSSGPNGR DMTVEEGAAA LQ RDLRLAK RLGFRFVRPK IGVVSSDLIP HPIWTEVVEA SLPLAEELDV IICPEIHSPT PIKHEVVDDY IALIRRTGTK HFG LLLDTG IFQDRPIPLK PGELPGQRPA FLDGIHVDPN DVFDVIENVV FIQAKFHDID EELDDKQIPW EPVLKALKDA GYTG YLSSE YEGEREPWRS IEQVRRQHSL IRQIADRLAE

UniProtKB: C-deglycosylation enzyme beta subunit

-
Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5 / Details: 25 mM HEPES pH 7.5, 150 mM NaCl, 0.15 mM MnCl2
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
Detailsmonodisperse sample

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
DetailsData collected on the Karolinska Institutet's Krios G3i equipped with a cold-FEG
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 734119
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.3.1) / Details: Ab-initio
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: X-ray model of the same sample
Output model

PDB-8un2:
Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type (cryo-EM)

+
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://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