[English] 日本語
Yorodumi
- PDB-2n5c: Solution NMR structure of the lasso peptide chaxapeptin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n5c
TitleSolution NMR structure of the lasso peptide chaxapeptin
Componentschaxapeptin
KeywordsCELL INVASION / chaxapeptin / RiPPs / genome mining / Atacama Desert / Streptomyces
Function / homologyLs3A-pre-pro-peptide
Function and homology information
Biological speciesStreptomyces leeuwenhoekii (bacteria)
MethodSOLUTION NMR / simulated annealing, distance geometry
AuthorsElsayed, S.S. / Trusch, F. / Deng, H. / Raab, A. / Prokes, I. / Busarakam, K. / Asenjo, J.A. / Andrews, B.A. / van West, P. / Bull, A.T. ...Elsayed, S.S. / Trusch, F. / Deng, H. / Raab, A. / Prokes, I. / Busarakam, K. / Asenjo, J.A. / Andrews, B.A. / van West, P. / Bull, A.T. / Goodfellow, M. / Yi, Y. / Ebel, R. / Jaspars, M. / Rateb, M.E.
CitationJournal: J.Org.Chem. / Year: 2015
Title: Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert.
Authors: Elsayed, S.S. / Trusch, F. / Deng, H. / Raab, A. / Prokes, I. / Busarakam, K. / Asenjo, J.A. / Andrews, B.A. / van West, P. / Bull, A.T. / Goodfellow, M. / Yi, Y. / Ebel, R. / Jaspars, M. / Rateb, M.E.
History
DepositionJul 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: chaxapeptin


Theoretical massNumber of molelcules
Total (without water)1,6341
Polymers1,6341
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)15 / 20structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide chaxapeptin


Mass: 1633.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Isolate from hyper-arid Atacama Desert / Source: (natural) Streptomyces leeuwenhoekii (bacteria) / Strain: C58 / References: UniProt: A0A0F7VRL1*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 1H
1211D 13C
1311D DEPTQ
1412D 1H-15N HSQC
1512D 1H-1H COSY
1612D 1H-1H TOCSY
1712D HMBC
1812D 1H-1H NOESY
1913D 1H-15N TOCSY

-
Sample preparation

DetailsContents: 4 mM chaxapeptin, 100% DMSO / Solvent system: 100% DMSO
SampleConc.: 4 mM / Component: chaxapeptin-1
Sample conditionsPressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Varian VNMRSVarianVNMRS6002

-
Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
WHAT IF11.12.31Vriendgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 156 / NOE intraresidue total count: 34 / NOE long range total count: 62 / NOE medium range total count: 14 / NOE sequential total count: 46
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 20 / Conformers submitted total number: 15

+
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