[English] 日本語
Yorodumi
- EMDB-37331: Cryo-EM structure of the DegQ dodecamer with a lysozyme -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37331
TitleCryo-EM structure of the DegQ dodecamer with a lysozyme
Map data
Sample
  • Complex: DegQ in complex with lysozyme
    • Other: DegQ-lysozyme complex
KeywordsSeine protease / HYDROLASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsLee I-G / Jeon H
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other privateLF-RSP2022-02 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of bacterial serine protease
Authors: Lee I-G / Jeon H
History
DepositionAug 29, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37331.png

Downloads & links

-
Map

FileDownload / File: emd_37331.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.)
0.85 Å/pix.
x 360 pix.
= 305.28 Å		0.85 Å/pix.
x 360 pix.
= 305.28 Å		0.85 Å/pix.
x 360 pix.
= 305.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10390915 - 0.20929107
Average (Standard dev.)0.0002768475 (±0.011708032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 305.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_37331_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37331_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DegQ in complex with lysozyme

EntireName: DegQ in complex with lysozyme
Components
  • Complex: DegQ in complex with lysozyme
    • Other: DegQ-lysozyme complex

-
Supramolecule #1: DegQ in complex with lysozyme

SupramoleculeName: DegQ in complex with lysozyme / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: DegQ-lysozyme complex

MacromoleculeName: DegQ-lysozyme complex / type: other / ID: 1 / Classification: other
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFEG LGSGVIINAS KGYVLTNNHV INQAQKISIQ LNDGREFDAK LIGSDDQSDI ALLQIQNPSK LTQIAIADSD KLRVGDFAVA ...String:
MKKQTQLLSA LALSVGLTLS ASFQAVASIP GQVADQAPLP SLAPMLEKVL PAVVSVRVEG TASQGQKIPE EFKKFFGDDL PDQPAQPFEG LGSGVIINAS KGYVLTNNHV INQAQKISIQ LNDGREFDAK LIGSDDQSDI ALLQIQNPSK LTQIAIADSD KLRVGDFAVA VGNPFGLGQT ATSGIVSALG RSGLNLEGLE NFIQTDASIN RGNSGGALLN LNGELIGINT AILAPGGGSV GIGFAIPSNM ARTLAQQLID FGEIKRGLLG IKGTEMSADI AKAFNLDVQR GAFVSEVLPG SGSAKAGVKA GDIITSLNGK PLNSFAELRS RIATTEPGTK VKLGLLRNGK PLEVEVTLDT STSSSASAEM ITPALEGATL SDGQLKDGGK GIKIDEVVKG SPAAQAGLQK DDVIIGVNRD RVNSIAEMRK VLAAKPAIIA LQIVRGNESI YLLMR
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326131
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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