[English] 日本語
Yorodumi
- PDB-8s2a: NMR structure of xantholysin A in micellar DPC solution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s2a
TitleNMR structure of xantholysin A in micellar DPC solution
ComponentsXantholysin A
KeywordsSURFACTANT PROTEIN / Non-ribosomal polypeptide / Cyclic lipodepsipeptide / Antimicrobial peptide / Biosurfactant
Function / homology: / polypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKovacs, B. / Geudens, N. / Martins, J.C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)EOS project G0G3118N (EOS ID 30650620) Belgium
CitationJournal: To be published
Title: NMR structure of xantholysin A in micellar DPC solution
Authors: Kovacs, B. / Geudens, N. / Martins, J.C.
History
DepositionFeb 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xantholysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8122
Polymers1,6241
Non-polymers1881
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodOccasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1)
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Polypeptide(D) Xantholysin A


Mass: 1623.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 1) The polypeptide chain of xantholysin A consists of 14 amino acids. 2) The N-terminal amino acid (Leu) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as ...Details: 1) The polypeptide chain of xantholysin A consists of 14 amino acids. 2) The N-terminal amino acid (Leu) is acylated with an (R)-3-hydroxy-decanoic acid (IG8) moeity which is indicated as the first residue. 3) The depsi (ester) bond is established between the ILE15 carboxyl and SER8 side-chain OH group.
Source: (natural) Pseudomonas putida (bacteria) / Strain: BW11M1
#2: Chemical ChemComp-IG8 / (3~{R})-3-oxidanyldecanoic acid


Mass: 188.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O3
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

DetailsType: solution
Contents: 3.2 mM xantholysin A, 162.9 mM [U-2H] DPC, 90% H2O/10% D2O
Details: Xantholysin A was dissolved in the micellar solution of uniformly deuterated dodecylphosphocholine (DPC-d38). Solvent: 10 mM Na2HPO4/NaH2PO4 buffer at pH 7.4.
Label: 1H / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.2 mMxantholysin Anatural abundance1
162.9 mMDPC[U-2H]1
Sample conditionsIonic strength: 26 (buffer only) mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz / Details: Prodigy Cryoprobe

-
Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberToolsCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
TopSpin3.xBruker Biospinprocessing
TopSpin3.xBruker Biospincollection
CcpNmr AnalysisVuister et al.peak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CcpNmr AnalysisVuister et al.chemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a ...Details: The lowest energy NMR structure issued from CNS was refined using unrestrained AMBER molecular dynamics simulations (against the ff14SB force field). Here, we modelled the interaction of a single peptide molecule with an explicit dodecylphosphocholine (DPC) micelle. The representative peptide conformation of the trajectory (=refined structure) was selected using cluster analysis. Solvent model: TIP3P. Occasional too-close contacts present in the NMR structure ensemble (structures #2-#11) are fully removed during the AMBER moleculary dynamics refinement (structure #1)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

+
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