[English] 日本語
Yorodumi
- SASDDG3: Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDDG3
SampleSolution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA
  • Sa0446 binding sequence 40bp (DNA), 40bp dsDNA
  • Transcriptional regulator Lrs14-like protein (protein), AbfR2, Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
Function / homologyTranscription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator Lrs14-like protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Contact author
  • Marian Vogt (University of Marburg, Marburg, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1781
Type: dummy / Radius of dummy atoms: 2.70 A / Chi-square value: 0.861
Search similar-shape structures of this assembly by Omokage search (details)
Model #1782
Type: dummy / Radius of dummy atoms: 2.70 A / Chi-square value: 0.830 / P-value: 0.000013
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA
Specimen concentration: 0.63 mg/ml / Entity id: 869 / 919
BufferName: 300 mM NaCl, 20 mM HEPES, pH 7.5 / pH: 7.5
Entity #869Name: 40bp dsDNA / Type: DNA / Description: Sa0446 binding sequence 40bp / Formula weight: 24.721 / Num. of mol.: 1
Sequence:
GTAGTAAGAT TTAAAAAAAC ATACTAAGAT ATAAATTAAC GTTAATTTAT ATCTTAGTAT GTTTTTTTAA ATCTTACTAC
Entity #919Name: AbfR2 / Type: protein / Description: Transcriptional regulator Lrs14-like protein / Formula weight: 16.368 / Num. of mol.: 2
Source: Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
References: UniProt: Q4J9G1
Sequence:
MGSSHHHHHH SQDPNSMETV LQIPYQKKTQ IEKLLEFMYG LNEKEVQLIF RLLYSDTKLN IEELAEEFKV SKALISKSLS ELANKGLIER EKVSNEGRKG RPIYVYYVDR EQLFKRISRD LEELVQASIA KLKEYIFKS

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.124 Å
DetectorName: Pilatus 1M
Scan
Title: Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2) in Complex with DNA
Measurement date: Nov 5, 2016 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /
MinMax
Q0.0348 4.9439
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 470 /
MinMax
Q0.114886 2.32447
P(R) point1 470
R0 12.8
Result
Type of curve: merged
ExperimentalStandardPorod
MW41.981 kDa67.74 kDa-
Volume--60.38 nm3

P(R)GuinierGuinier error
Forward scattering, I068.09 67.74 0.17
Radius of gyration, Rg3.561 nm3.44 nm0.81

MinMax
D-12.8
Guinier point18 64

+
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