[English] 日本語
Yorodumi
- EMDB-42680: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42680
TitleCryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43
Map datadeepenhancer map
Sample
  • Complex: Tetrameric GH43 structure
    • Protein or peptide: Beta-xylosidaseXylan 1,4-b-xylosidase
  • Ligand: CALCIUM IONCalcium
KeywordsGH43 / Enterobacter / Beta-Xylosidase / EcXyl43 / HYDROLASE
Function / homologyBeta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Beta-xylosidase
Function and homology information
Biological speciesEnterobacter hormaechei (CDC Enteric Group 75)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsBriganti L / Godoy AS / Capetti CCM / Portugal RV / Polikarpov I
Funding support Brazil, 1 items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
CitationJournal: To Be Published
Title: Cryo-EM structure of an Enterobacter GH43 Beta-Xylosidase: EcXyl43
Authors: Briganti L / Godoy AS / Polikarpov I
History
DepositionNov 8, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42680.png

Downloads & links

-
Map

FileDownload / File: emd_42680.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdeepenhancer map
Voxel sizeX=Y=Z: 0.67 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.015794883 - 1.594079
Average (Standard dev.)0.0019094717 (±0.03095262)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: cryosparc refinement map

Fileemd_42680_additional_1.map
Annotationcryosparc refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: mask

Fileemd_42680_additional_2.map
Annotationmask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half B

Fileemd_42680_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half A

Fileemd_42680_half_map_2.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tetrameric GH43 structure

EntireName: Tetrameric GH43 structure
Components
  • Complex: Tetrameric GH43 structure
    • Protein or peptide: Beta-xylosidaseXylan 1,4-b-xylosidase
  • Ligand: CALCIUM IONCalcium

-
Supramolecule #1: Tetrameric GH43 structure

SupramoleculeName: Tetrameric GH43 structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Enterobacter hormaechei (CDC Enteric Group 75)

-
Macromolecule #1: Beta-xylosidase

MacromoleculeName: Beta-xylosidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Enterobacter hormaechei (CDC Enteric Group 75)
Molecular weightTheoretical: 61.000953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEITNPILTG FNPDPSLCRQ GEDYYIATST FEWFPGVRIY HSRDLKNWTL VSTPLDRVSM LDMKGNPDSG GIWAPCLSYA DGKFWLLYT DVKIVDSPWK NGRNFLVTAP SIEGPWSEPI PMGNGGFDPS LFHDDDGRKY YLYRPWGPRH HSNPHNTIVM Q EFDPQTGT ...String:
MEITNPILTG FNPDPSLCRQ GEDYYIATST FEWFPGVRIY HSRDLKNWTL VSTPLDRVSM LDMKGNPDSG GIWAPCLSYA DGKFWLLYT DVKIVDSPWK NGRNFLVTAP SIEGPWSEPI PMGNGGFDPS LFHDDDGRKY YLYRPWGPRH HSNPHNTIVM Q EFDPQTGT LSPERKTLFT GTPLCYTEGA HLYRHAGWYY LMVAEGGTSY EHAVVVLRAK TIDGPYELHP DVTMMTSWHL PE NPLQKSG HGSLLQTHTG EWYMAYLTSR PLRLPGVPLL ASGGRGYCPL GRETGIARIE WRDGWPYVEG GKHAQLTVKG PQV AEQPAA VQGSWRDDFD GSTLDPELQT LRIPFDDTLG SLTARPGYLR LYGNDSLNST FTQSTVARRW QHFIFRAETR MQFS PVHFQ QSAGLTCYYN SKNWSYCFVD YEEGQGRTIK VIQLDHNVPS WPLHEQPIPV PEQAESVWLR VDVDRLVYRY SYSFD GETW HAVPVTYEAW KLSDDYIGGR GFFTGAFVGL HCEDISGDGC HADFDYFTYE PA

UniProtKB: Beta-xylosidase

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7k1r

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 438836
FSC plot (resolution estimation)

+
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