[English] 日本語
Yorodumi
- PDB-2igz: NMR structure of the sterol-dependent antifungal antibiotic bacil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2igz
TitleNMR structure of the sterol-dependent antifungal antibiotic bacillomycin Lc
ComponentsBACILLOMYCIN L-3
KeywordsANTIBIOTIC / ITURINS / ANTIFUNGAL / CYCLOPEPTIDE / LIPOPEPTIDE / SURFACTANT BACILLOMYCIN
Function / homologyBacillomycin Lc / :
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsVolpon, L. / Tsan, P. / Besson, F. / Lancelin, J.M.
Citation
Journal: Spectrochim Acta a Mol.Biomol.Spectrosc. / Year: 2007
Title: NMR Structure Determination of a Synthetic Analogue of Bacillomycin Lc Reveals the Strategic Role of L-Asn1 in the Natural Iturinic Antibiotics.
Authors: Volpon, L. / Tsan, P. / Majer, Z. / Vass, E. / Hollosi, M. / Noguera, V. / Lancelin, J.M. / Besson, F.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: NMR Structure of Active and Inactive Forms of the Sterol-Dependent Antifungal Antibiotic Bacillomycin L
Authors: Volpon, L. / Besson, F. / Lancelin, J.M.
History
DepositionSep 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACILLOMYCIN L-3


Theoretical massNumber of molelcules
Total (without water)1,0531
Polymers1,0531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 50STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1

-
Components

#1: Protein/peptide BACILLOMYCIN L-3


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1053.165 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: BACILLOMYCIN LC IS A CYCLIC HEPTA-LIPOPETIDE WITH 7 AMINO-ACIDS OF CONFIGURATION LDDLLDL AND ONE D-BETA-AMINO CARBOXYLIC ACID. THE FATTY ACID IS LINKED VIA A PEPTID BOND TO BOTH RESIDUES 2 AND 8.
Source: (synth.) BACILLUS SUBTILIS (bacteria) / References: NOR: NOR00781, Bacillomycin Lc
Compound detailsBACILLOMYCIN LC IS A CYCLIC HEPTA-LIPOPETIDE. HERE, BACILLOMYCIN IS REPRESENTED BY THE SEQUENCE (SEQRES)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D-TOCSY (HOHAHA)
1312D NOESY
1412D-ROESY
1511H-13C HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

-
Sample preparation

DetailsContents: 3MM BACILLOMYCIN LC IN 100% DMSO-D6
Sample conditionsPressure: AMBIENT / Temperature: 292 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR software
NameDeveloperClassification
CHARMM 22BROOKS,BRUCCOLERI,OLAFSON,STATES,SWAMINATHAN, KARPLUSrefinement
X-PLOR 3.851structure solution
XWINNMRstructure solution
GIFA 4.0structure solution
MOLMOLstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 74 RESTRAINTS, 71 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 3 DIHEDRAL ANGLE RESTRAINTS. THE 19 STRUCTURES WERE DIVIDED INTO TWO FAMILIES OF SIMILAR ENERGY ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 74 RESTRAINTS, 71 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 3 DIHEDRAL ANGLE RESTRAINTS. THE 19 STRUCTURES WERE DIVIDED INTO TWO FAMILIES OF SIMILAR ENERGY WHICH ESSENTIALLY DIFFER IN THE NUMBER AND TYPE OF TURNS. THE TWO FAMILIES ARE S1 (STRUCTURES 1-12) AND S2 (STRUCTURES 13-19).
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 19

+
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