[English] 日本語
Yorodumi
- PDB-6vjq: Solution NMR structure of Prochlorosin 2.1 produced by Prochloroc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vjq
TitleSolution NMR structure of Prochlorosin 2.1 produced by Prochlorococcus MIT 9313
ComponentsProchlorosin 2.1
KeywordsUNKNOWN FUNCTION / lanthipeptide / cyclic peptide / posttranslational modification / RiPP
Function / homologyNif11 domain / Nif11-like leader peptide / Nif11 domain / transferase activity / Possible Formyl transferase
Function and homology information
Biological speciesProchlorococcus marinus str. MIT 9313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBobeica, S.C. / van der Donk, W.A. / Zhu, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM058822 United States
Citation
Journal: Chem Sci / Year: 2020
Title: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.
Authors: Bobeica, S.C. / Zhu, L. / Acedo, J.Z. / Tang, W. / van der Donk, W.A.
#1: Journal: Chem Sci / Year: 2020
Title: Correction: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.
Authors: Bobeica, S.C. / Zhu, L. / Acedo, J.Z. / Tang, W. / van der Donk, W.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Catalytic promiscuity in the biosynthesis of cyclic peptide secondary metabolites in planktonic marine cyanobacteria.
Authors: Li, B. / Sher, D. / Kelly, L. / Shi, Y. / Huang, K. / Knerr, P.J. / Joewono, I. / Rusch, D. / Chisholm, S.W. / van der Donk, W.A.
#3: Journal: Nat.Chem.Biol. / Year: 2013
Title: The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry.
Authors: Tang, W. / van der Donk, W.A.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2017
Title: Evolutionary radiation of lanthipeptides in marine cyanobacteria.
Authors: Cubillos-Ruiz, A. / Berta-Thompson, J.W. / Becker, J.W. / van der Donk, W.A. / Chisholm, S.W.
#5: Journal: Biochemistry / Year: 2012
Title: Structural characterization of four prochlorosins: a novel class of lantipeptides produced by planktonic marine cyanobacteria.
Authors: Tang, W. / van der Donk, W.A.
History
DepositionJan 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 9, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / pdbx_entity_instance_feature ...atom_site / pdbx_entity_instance_feature / pdbx_nmr_representative / pdbx_struct_assembly / pdbx_validate_torsion / struct_conf / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_nmr_representative.selection_criteria / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_conn.pdbx_dist_value
Description: Chirality error
Details: Residue DBB 4 should have been (S) configuration at CB. An additional improper angle was added to the XPLOR patch command to ensure (S) stereochemistry at CB of DBB residues involved in DL ...Details: Residue DBB 4 should have been (S) configuration at CB. An additional improper angle was added to the XPLOR patch command to ensure (S) stereochemistry at CB of DBB residues involved in DL (methyl)lanthionine linkages is maintained.
Provider: author / Type: Coordinate replacement
Revision 2.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Revision 2.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 3.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn
Item: _database_2.pdbx_DOI / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prochlorosin 2.1


Theoretical massNumber of molelcules
Total (without water)2,7621
Polymers2,7621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Prochlorosin 2.1


Mass: 2762.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus str. MIT 9313 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q7TUK2*PLUS
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
232isotropic12D 1H-1H TOCSY
242isotropic12D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM Prochlorosin 2.1, 90% H2O/10% D2OPcn2.190% H2O/10% D2O
solution23 mM Prochlorosin 2.1, 100% D2OPcn2.1_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMProchlorosin 2.1natural abundance1
3 mMProchlorosin 2.1natural abundance2
Sample conditions

Ionic strength: 0 Not defined / Ionic strength err: _ / pH: 6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: _ / Temperature: 296 K / Temperature err: 0.1

Conditions-IDLabel
1Pcn2.1_details
2Pcn2.1_D2O_details

-
NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 750 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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