[English] 日本語
Yorodumi
- PDB-1h9c: NMR structure of cysteinyl-phosphorylated enzyme IIB of the N,N'-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h9c
TitleNMR structure of cysteinyl-phosphorylated enzyme IIB of the N,N'-diacetylchitobiose specific phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli.
ComponentsPTS SYSTEM, CHITOBIOSE-SPECIFIC IIB COMPONENT
KeywordsTRANSFERASE / ENZYME IIB-CHITOBIOSE / PHOSPHOTRANSFERASE SYSTEM / SUGAR TRANSPORT / PHOSPHORYLATION / IIB- CELLOBIOSE
Function / homology
Function and homology information


protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase / protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / cytosol
Similarity search - Function
Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system N,N'-diacetylchitobiose-specific EIIB component / PTS system N,N'-diacetylchitobiose-specific EIIB component
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsAb, E. / Schuurman-Wolters, G.K. / Nijlant, D. / Dijkstra, K. / Saier, M.H. / Robillard, G.T. / Scheek, R.M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: NMR Structure of Cysteinyl-Phosphorylated Enzyme Iib of the N,N'-Diacetylchitobiose Specific Phosphoenolpyruvate-Dependentphosphotransferase System of Escherichia Coli
Authors: Ab, E. / Schuurman-Wolters, G.K. / Nijlant, D. / Dijkstra, K. / Saier, M.H. / Robillard, G.T. / Scheek, R.M.
#1: Journal: Protein Sci. / Year: 1997
Title: The NMR Side-Chain Assignments and Solution Structure of Enzyme Iibcellobiose of the Phosphoenolpyruvate-Dependent Phosphotransferase System of Escherichia Coli
Authors: Ab, E. / Schuurman-Wolters, G. / Reizer, J. / Saier, M.H. / Dijkstra, K. / Scheek, R.M. / Robillard, G.T.
#2: Journal: Protein Sci. / Year: 1994
Title: Enzyme Iibcellobiose of the Phosphoenol-Pyruvate-Dependent Phosphotransferase System of Escherichia Coli: Backbone Assignment and Secondary Structure Determined by Three-Dimensional NMR Spectroscopy
Authors: Ab, E. / Schuurman-Wolters, G.K. / Saier, M.H. / Reizer, J. / Jacuinod, M. / Roepstorff, P. / Dijkstra, K. / Scheek, R.M. / Robillard, G.T.
#3: Journal: Genetics / Year: 1990
Title: Characterization and Nucleotide Sequence of the Cryptic Cel Operon of Escherichia Coli K12
Authors: Parker, L.L. / Hall, B.G.
#4: Journal: Res.Microbiol. / Year: 1990
Title: The Cellobiose Permease of Escherichia Coli Consists of Three Proteins and is Homologous to the Lactose Permease of Staphylococcus Aureus
Authors: Reizer, J. / Reizer, A. / Saier Jr, M.H.
History
DepositionMar 7, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS SYSTEM, CHITOBIOSE-SPECIFIC IIB COMPONENT


Theoretical massNumber of molelcules
Total (without water)11,5191
Polymers11,5191
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)9 / 33TARGET-FUNCTION, R-FACTOR, NUMBER OF VIOLATIONS
RepresentativeModel #1

-
Components

#1: Protein PTS SYSTEM, CHITOBIOSE-SPECIFIC IIB COMPONENT / EIIB-CEL / EIIB-CHB


Mass: 11519.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATION AT RESIDUE CYS10 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: W3110 / Cellular location: CYTOPLASM / Gene: CHBB [PREV CELA] / Plasmid: PJR-BLIIB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110
References: UniProt: P17409, UniProt: P69795*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase
Compound detailsCOMPONENT OF THE PHOSPHOENOLPYRUVATE-DEPENDENT SUGAR PHOSPHOTRANSFERASE SYSTEM (PTS)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY

-
Sample preparation

Sample conditionspH: 7 / Pressure: 1 atm / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
GROMACSVAN DER SPOELrefinement
SNARFstructure solution
DDDstructure solution
GROMACSstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: TARGET-FUNCTION, R-FACTOR, NUMBER OF VIOLATIONS
Conformers calculated total number: 33 / Conformers submitted total number: 9

+
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