[English] 日本語
Yorodumi
- PDB-8dfz: NMR shows why a small chemical change almost abolishes the antimi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dfz
TitleNMR shows why a small chemical change almost abolishes the antimicrobial activity of GccF
ComponentsBacteriocin glycocin F
KeywordsANTIMICROBIAL PROTEIN / GccF / antimicrobial / bacteriostatic
Function / homologykilling of cells of another organism / defense response to Gram-positive bacterium / extracellular region / Bacteriocin glycocin F
Function and homology information
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHarjes, E. / Edwards, P.J.B. / Norris, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: NMR Shows Why a Small Chemical Change Almost Abolishes the Antimicrobial Activity of Glycocin F.
Authors: Harjes, E. / Edwards, P.J.B. / Bisset, S.W. / Patchett, M.L. / Jameson, G.B. / Yang, S.H. / Navo, C.D. / Harris, P.W.R. / Brimble, M.A. / Norris, G.E.
History
DepositionJun 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriocin glycocin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2633
Polymers4,8201
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Bacteriocin glycocin F / GccF


Mass: 4820.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: gccF / Production host: Lactiplantibacillus plantarum (bacteria) / References: UniProt: E9K9Z1
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D DQF-COSY
141isotropic12D 1H-13C HSQC
151isotropic1HMBC
161isotropic13D 1H-13C TOCSY

-
Sample preparation

DetailsType: solution
Contents: 1 mM natural abundabnce GccF modified, 95% H2O/5% D2O
Details: 40% d3-acetonitrile / water with 0.2% d3-acetic acid
Label: natural abbundance / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: GccF modified / Isotopic labeling: natural abundabnce
Sample conditionsIonic strength: 0 mM / Label: condition1 / pH: 0 Not defined / Pressure: 1 atm / Temperature: 307 K

-
NMR measurement

NMR spectrometerType: Bruker Bruker Avance / Manufacturer: Bruker / Model: Bruker Avance / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
YASARAElmer Kriegerrefinement
YASARAElmer Kriegerstructure calculation
CARAKeller and Wuthrichchemical shift assignment
ATNOSHermannpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

+
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