[English] 日本語
Yorodumi
- PDB-1pux: NMR Solution Structure of BeF3-Activated Spo0F, 20 conformers -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pux
TitleNMR Solution Structure of BeF3-Activated Spo0F, 20 conformers
ComponentsSporulation initiation phosphotransferase F
KeywordsTRANSFERASE / sporulation / (beta/alpha)5 barrel / response regulator / phosphorelay / beryllofluoride / two-component systems
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / kinase activity / phosphorylation / metal ion binding / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sporulation initiation phosphotransferase F
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing
AuthorsGardino, A.K. / Volkman, B.F. / Cho, H.S. / Lee, S.Y. / Wemmer, D.E. / Kern, D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The NMR solution structure of BeF(3)(-)-activated Spo0F reveals the conformational switch in a phosphorelay system.
Authors: Gardino, A.K. / Volkman, B.F. / Cho, H.S. / Lee, S.Y. / Wemmer, D.E. / Kern, D.
History
DepositionJun 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sporulation initiation phosphotransferase F


Theoretical massNumber of molelcules
Total (without water)14,2451
Polymers14,2451
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Sporulation initiation phosphotransferase F / Stage 0 sporulation protein F


Mass: 14244.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SPO0F / Plasmid: pET21a (NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) with pACYC
References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: This structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

DetailsContents: Uniform labeling with 15N and 13C
Solvent system: 1 mM Spo0F, 20 mM HEPES, 50 mM MgCl2, 6 mM BeCl2, and 60 mM NaF, 10% D20
Sample conditionsIonic strength: 50 mM MgCl2, 6 mM BeCl2, 60 mM NaF / pH: 6.85 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, Pstructure solution
DYANA1.5Guntert, Prefinement
XEASY1.3.12Bartels, Cdata analysis
RefinementMethod: Torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Structure based on a total of 1,835 distance constraints (obtained from 4,221 NOE crosspeaks), including 602 intraresidual, 504 short-range, 310 medium-range, and 383 long-range constraints ...Details: Structure based on a total of 1,835 distance constraints (obtained from 4,221 NOE crosspeaks), including 602 intraresidual, 504 short-range, 310 medium-range, and 383 long-range constraints as well as 165 dihedral angle restraints for a total of 2,000 restraints. DYANA 1.5 anneal command (20000) steps was used to generate 60 conformers. 20 lowest target function structures were analyzed.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 60 / 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