[English] 日本語
Yorodumi
- PDB-1q71: The structure of microcin J25 is a threaded sidechain-to-backbone... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q71
TitleThe structure of microcin J25 is a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone
Componentsmicrocin J25
KeywordsANTIBIOTIC / microcin J25 / mccj25 / sidechain-to-backbone link / antimicrobial peptide / ANTIMICROBIAL PROTEIN
Function / homologykilling of cells of another organism / defense response to bacterium / extracellular region / Microcin J25 / Microcin J25
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Structures were calculated by torsion angle dynamics, refined in a water shell using Cartesian dynamics within CNS.
AuthorsRosengren, K.J. / Clark, R. / Daly, N.L. / Goransson, U. / Jones, A. / Craik, D.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone.
Authors: Rosengren, K.J. / Clark, R.J. / Daly, N.L. / Goransson, U. / Jones, A. / Craik, D.J.
History
DepositionAug 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: microcin J25


Theoretical massNumber of molelcules
Total (without water)2,1261
Polymers2,1261
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)20 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide microcin J25


Type: Polypeptide / Class: Inhibitor / Mass: 2126.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcjA / Plasmid: pTUC202 / Production host: Escherichia coli (E. coli) / Strain (production host): MC4100 / References: UniProt: Q9X2V7, Microcin J25

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131E-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 0.3 mg of microcin J25 / Solvent system: 100% CD3OH
Sample conditionsIonic strength: 0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AvanceBrukerAvance5002

-
Processing

NMR software
NameVersionDeveloperClassification
XWINNMR3.1Brukercollection
XEASY1.3.7Eccles, C., Guntert, P., Billeter, M. and Wuthrich, K.data analysis
DYANA1.5Guntert, P., Mumenthaler, C. and Wuthrich, K.structure solution
CNS1Brunger, A.T. et al.refinement
RefinementMethod: Structures were calculated by torsion angle dynamics, refined in a water shell using Cartesian dynamics within CNS.
Software ordinal: 1
Details: Preliminary structures were generated by torsion angle dynamics using CNS. Structures were subsequently subjected to further molecular dynamics and energy minimisation in a water shell using ...Details: Preliminary structures were generated by torsion angle dynamics using CNS. Structures were subsequently subjected to further molecular dynamics and energy minimisation in a water shell using protocols from ARIA within CNS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / 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://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