[English] 日本語
Yorodumi
- SASDEC8: Bacillus thuringiensis LexA repressor bound to Bacteriophage pGIL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDEC8
SampleBacillus thuringiensis LexA repressor bound to Bacteriophage pGIL01 gp7 (Bt_LexA_GIL01_gp7)
  • Bacillus thuringiensis LexA repressor (protein), LexA, Bacillus thuringiensis
  • Bacteriophage pGIL01 gp7 (protein), gp7, Bacteriophage pGIL01
Function / homology
Function and homology information


repressor LexA / SOS response / DNA replication / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / proteolysis / DNA binding
Similarity search - Function
LexA repressor, DNA-binding domain / Transcription regulator LexA / LexA DNA binding domain / Peptidase S24, LexA-like / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
LexA repressor / Gene regulator
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
Bacteriophage pGIL01
CitationDate: 2019 May
Title: Structural Insights into Bacteriophage GIL01 gp7 Inhibition of Host LexA Repressor
Authors: Caveney N / Pavlin A / Caballero G / Bahun M / Hodnik V / de Castro L / Fornelos N / Butala M
Contact author
  • Nathanael Caveney (University of British Columbia)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2676
Type: atomic
Comment: I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex
Chi-square value: 6.158
Search similar-shape structures of this assembly by Omokage search (details)
Model #2677
Type: atomic
Comment: I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex in SREFLEX, restrained
Chi-square value: 2.580 / P-value: 0.000002
Search similar-shape structures of this assembly by Omokage search (details)
Model #2678
Type: atomic
Comment: I-TASSER, ClusPro, ModLoop model of LexA-gp7 complex in SREFLEX, unrestrained
Chi-square value: 1.899 / P-value: 0.000040
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Bacillus thuringiensis LexA repressor bound to Bacteriophage pGIL01 gp7 (Bt_LexA_GIL01_gp7)
Specimen concentration: 0.75-12.00 / Entity id: 1376 / 1377
BufferName: 20 mM Hepes, 300 mM NaCl, 10% glycerol, / pH: 8
Entity #1376Name: LexA / Type: protein / Description: Bacillus thuringiensis LexA repressor / Formula weight: 23.394 / Num. of mol.: 2 / Source: Bacillus thuringiensis / References: UniProt: A0A2B4EEI3
Sequence: MLENMEKLTK RQQDILDFIK LKVQEKGYPP SVREIGQAVG LASSSTVHGH LSRLEEKGYI RRDPTKPRAI EILGEDRMDT ETQSVIQVPI VGKVTAGLPI TAVESVEEHF PLPASIVSGA DQVFMLRISG DSMIEAGIFD GDLVVVRQQQ SAYNGEIVVA LTEDNEATVK ...Sequence:
MLENMEKLTK RQQDILDFIK LKVQEKGYPP SVREIGQAVG LASSSTVHGH LSRLEEKGYI RRDPTKPRAI EILGEDRMDT ETQSVIQVPI VGKVTAGLPI TAVESVEEHF PLPASIVSGA DQVFMLRISG DSMIEAGIFD GDLVVVRQQQ SAYNGEIVVA LTEDNEATVK RFYKEKDHFR LQPENSSLEP IILKQVSVIG KVIGVYRDLH
Entity #1377Name: gp7 / Type: protein / Description: Bacteriophage pGIL01 gp7 / Formula weight: 5.921 / Num. of mol.: 4 / Source: Bacteriophage pGIL01 / References: UniProt: Q7WSG2
Sequence:
MRDKLLDFII ELSQSSKQVV SKSYVIDRLM QVTKEDYKEL EKNVEGKKDD

-
Experimental information

BeamInstrument name: University of British Columbia Rigaku BioSAXS-2000
City: Vancouver / 国: Canada / Type of source: X-ray in house / Wavelength: 0.154 Å
DetectorName: Rigaku HyOix-3000 / Type: Hybrid Pixel Array Detector / Pixsize x: 100 mm
Scan
Title: Bacillus thuringiensis LexA repressor bound to Bacteriophage pGIL01 gp7 (Bt_LexA_GIL01_gp7)
Measurement date: Aug 25, 2017 / Storage temperature: 6 °C / Cell temperature: 6 °C / Exposure time: 300 sec. / Number of frames: 12 / Unit: 1/A /
MinMax
Q0.0117 0.6422
ResultExperimental MW: 108.2 kDa / I0 from Guinier: 1.53 / Rg from Guinier: 4.391 nm / Type of curve: merged

+
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