[English] 日本語
Yorodumi
- PDB-1uxc: FRUCTOSE REPRESSOR DNA-BINDING DOMAIN, NMR, MINIMIZED STRUCTURE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uxc
TitleFRUCTOSE REPRESSOR DNA-BINDING DOMAIN, NMR, MINIMIZED STRUCTURE
ComponentsFRUCTOSE REPRESSOR
KeywordsTRANSCRIPTION REGULATION / DNA-BINDING PROTEIN / FRUCTOSE REPRESSOR / LACI FAMILY
Function / homology
Function and homology information


response to fructose / regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) ...D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Catabolite repressor/activator
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsPenin, F. / Geourjon, C. / Montserret, R. / Bockmann, A. / Lesage, A. / Yang, Y. / Bonod-Bidaud, C. / Cortay, J.C. / Negre, D. / Cozzone, A.J. / Deleage, G.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR.
Authors: Penin, F. / Geourjon, C. / Montserret, R. / Bockmann, A. / Lesage, A. / Yang, Y.S. / Bonod-Bidaud, C. / Cortay, J.C. / Negre, D. / Cozzone, A.J. / Deleage, G.
#1: Journal: FEBS Lett. / Year: 1996
Title: Rapid Estimation of Relative Amide Proton Exchange Rates of 15 N-Labelled Proteins by a Straightforward Water Selective Noesy-Hsqc Experiment
Authors: Bockmann, A. / Penin, F. / Guittet, E.
#2: Journal: Gene / Year: 1995
Title: Overproduction, Purification and Structural Characterization of the Functional N-Terminal DNA-Binding Domain of the Fru Repressor from Escherichia Coli K-12
Authors: Scarabel, M. / Penin, F. / Bonod-Bidaud, C. / Negre, D. / Cozzone, A.J. / Cortay, J.C.
History
DepositionDec 26, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FRUCTOSE REPRESSOR


Theoretical massNumber of molelcules
Total (without water)7,3961
Polymers7,3961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein FRUCTOSE REPRESSOR / FRUR (1-57)


Mass: 7396.483 Da / Num. of mol.: 1
Fragment: DNA-BINDING DOMAIN, RESIDUES 1 - 57, WITH LQHHHHHH ADDED AT C-TERMINUS
Mutation: INS(58-65), CLONING ARTIFACTS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: OVERPRODUCED IN FUSION WITH A LQHHHHHH SEQUENCE AT C-TERMINAL END, RESIDUES 58 - 65
Variant: K12 / Plasmid: PCB4 / Gene (production host): FRUR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACP1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 5.9 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR / Version: 3.1 / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 1

+
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