[English] 日本語
Yorodumi
- PDB-1iba: GLUCOSE PERMEASE (DOMAIN IIB), NMR, 11 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iba
TitleGLUCOSE PERMEASE (DOMAIN IIB), NMR, 11 STRUCTURES
ComponentsGLUCOSE PERMEASE
KeywordsPHOSPHOTRANSFERASE / PHOSPHOTRANSFERASE SYSTEM / SUGAR TRANSPORT / TRANSFERASE / PHOSPHORYLATION / TRANSMEMBRANE / INNER MEMBRANE
Function / homology
Function and homology information


protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / : / D-glucose import across plasma membrane / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / regulation of DNA-templated transcription ...protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / : / D-glucose import across plasma membrane / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / regulation of DNA-templated transcription / membrane / plasma membrane
Similarity search - Function
Glucose permease domain IIB / Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / : / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. ...Glucose permease domain IIB / Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / : / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system glucose-specific EIICB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsEberstadt, M. / Grdadolnik, S.G. / Gemmecker, G. / Kessler, H. / Buhr, A. / Erni, B.
Citation
Journal: Biochemistry / Year: 1996
Title: Solution structure of the IIB domain of the glucose transporter of Escherichia coli.
Authors: Eberstadt, M. / Grdadolnik, S.G. / Gemmecker, G. / Kessler, H. / Buhr, A. / Erni, B.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: The Glucose Transporter of Escherichia Coli. Assignment of the 1H, 13C and 15N Resonances and Identification of the Secondary Structure of the Soluble Iib Domain
Authors: Golic Grdadolnik, S. / Eberstadt, M. / Gemmecker, G. / Kessler, H. / Buhr, A. / Erni, B.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: The Glucose Transporter of Escherichia Coli
Authors: Buhr, A. / Flukiger, K. / Erni, B.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Cysteine Phosphorylation of the Glucose Transporter of Escherichia Coli
Authors: Meins, M. / Jeno, P. / Muller, D. / Richter, W.J. / Rosenbusch, J.P. / Erni, B.
#4: Journal: J.Biol.Chem. / Year: 1986
Title: Glucose-Permease of the Bacterial Phosphotransferase System. Gene Cloning, Overproduction, and Amino Acid Sequence of Enzyme Iiglc
Authors: Erni, B. / Zanolari, B.
History
DepositionMar 23, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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: GLUCOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)10,7521
Polymers10,7521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / -
Representative

-
Components

#1: Protein GLUCOSE PERMEASE


Mass: 10752.142 Da / Num. of mol.: 1 / Fragment: DOMAIN IIB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12, W3110 / Plasmid: PQBH / Gene (production host): PTSG / Production host: Escherichia coli (E. coli)
References: UniProt: P69786, protein-Npi-phosphohistidine-sugar phosphotransferase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR softwareName: DIANA / Version: 2.8 / Developer: GUNTERT, BRAUN, WUTHRICH / Classification: refinement
NMR ensembleConformers submitted total number: 11

+
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