[English] 日本語
Yorodumi
- PDB-9oil: Solution Structure of the Broadspectrum Bacteriocin Garvicin Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oil
TitleSolution Structure of the Broadspectrum Bacteriocin Garvicin Q
ComponentsPrepeptide GarQ
KeywordsANTIBIOTIC / Bacteriocin / Lactic Acid Bacteria / Alpha Helix / Mannose Phospho-transferase system
Function / homologyBacteriocin, class IId / Lactococcin-like family / Bacteriocin-type signal sequence / defense response to bacterium / extracellular region / Prepeptide GarQ
Function and homology information
Biological speciesLactococcus garvieae (lactic acid bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsMallett, T.M. / Lamer, T. / Aleksandrzak-Piekarczyk, T. / Mckay, R.T. / Sit, C.S. / Rainey, J.K. / Van Belkum, M. / Vederas, J.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2025
Title: Solution Structure of the Broad-Spectrum Bacteriocin Garvicin Q.
Authors: Mallett, T. / Lamer, T. / Aleksandrzak-Piekarczyk, T. / McKay, R.T. / Catenza, K. / Sit, C. / Rainey, J.K. / Towle-Straub, K.M. / Vederas, J.C. / van Belkum, M.J.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prepeptide GarQ


Theoretical massNumber of molelcules
Total (without water)5,3501
Polymers5,3501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Prepeptide GarQ


Mass: 5349.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus garvieae (lactic acid bacteria)
Strain: BCC 43578 / Gene: garQ / Plasmid: pSPIH6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6U5Y1
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic13D HN(CA)CB
131anisotropic13D 1H-15N TOCSY
141anisotropic13D 1H-15N NOESY
151anisotropic23D 1H-13C NOESY
161anisotropic23D (H)CCH-TOCSY

-
Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] Garvicin Q, trifluoroethanol/water
Details: 50 percent TFE in water, 100 microlitres. / Label: 13C,15N_Garvicin Q / Solvent system: trifluoroethanol/water
SampleConc.: 1.0 mM / Component: Garvicin Q / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 50 percent TFE in water, 100 microlitres. / Ionic strength: 0 Not defined / Ionic strength err: 0.1 / Label: GarQ_Conditions / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.1 / Temperature: 300.5 K / Temperature err: 2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian VNMRSVarianVNMRS7001University of Alberta, department of chemistry. Agilent/Varian VNMRS four-channel 600 MHz spectrometer with an autoxid HCN probe
Bruker AVIIIHDBrukerAVIIIHD8002QANUC 800, McGill University, Chemistry characterization facility

-
Processing

SoftwareName: THESEUS / Version: 3.3.0 / Classification: refinement
NMR software
NameVersionDeveloperClassification
CcpNmr Analysis3.2.12CCPNMRchemical shift assignment
X-PLOR NIH3.9.8Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOS-NAdriaan Baxgeometry optimization
PdbStatwwPDB Validation Servicerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

+
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