[English] 日本語
Yorodumi
- PDB-5msl: Solution structure of the B. subtilis anti-sigma-F factor, FIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5msl
TitleSolution structure of the B. subtilis anti-sigma-F factor, FIN
ComponentsAnti-sigma-F factor Fin
KeywordsTRANSCRIPTION / Zinc finger / bacillus subtilis / sigma factor / sporulation
Function / homologyAnti-sigma-F factor Fin / Anti-sigma-F factor Fin / sporulation resulting in formation of a cellular spore / regulation of gene expression / metal ion binding / cytoplasm / Anti-sigma-F factor Fin
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMartinez-Lumbreras, S. / Alfano, C. / Isaacson, R.L.
CitationJournal: Mol. Microbiol. / Year: 2017
Title: A novel RNA polymerase-binding protein that interacts with a sigma-factor docking site.
Authors: Wang Erickson, A.F. / Deighan, P. / Chen, S. / Barrasso, K. / Garcia, C.P. / Martinez-Lumbreras, S. / Alfano, C. / Krysztofinska, E.M. / Thapaliya, A. / Camp, A.H. / Isaacson, R.L. / Hochschild, A. / Losick, R.
History
DepositionJan 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 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_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_spectrometer.model / _struct_conn.pdbx_dist_value

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-sigma-F factor Fin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7522
Polymers8,6871
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6420 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

-
Components

#1: Protein Anti-sigma-F factor Fin / Suppressor of recU and recB SubA


Mass: 8686.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: fin, subA, yabK, BSU00540 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P37553
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic22D 1H-15N HSQC
123isotropic22D 1H-13C HSQC
133isotropic23D CBCA(CO)NH
143isotropic23D HN(CA)CB
153isotropic23D HNCO
163isotropic23D (H)CCH-TOCSY
172isotropic22D 1H-1H NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution2400 uM FIN, 10 mM potassium phosphate, 150 mM sodium chloride, 250 uM TCEP, 90% H2O/10% D2ONOESY90% H2O/10% D2O
solution3450 uM [U-100% 13C; U-100% 15N] FIN, 10 mM potassium phosphate, 150 mM sodium chloride, 250 uM TCEP, 90% H2O/10% D2O3Dexp90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMFINnatural abundance2
10 mMpotassium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
250 uMTCEPnatural abundance2
450 uMFIN[U-100% 13C; U-100% 15N]3
10 mMpotassium phosphatenatural abundance3
150 mMsodium chloridenatural abundance3
250 uMTCEPnatural abundance3
Sample conditionsIonic strength: 166 mM / Label: conditions / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: medoid
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