[English] 日本語
Yorodumi
- PDB-5iej: Solution structure of the BeF3-activated conformation of SdrG fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iej
TitleSolution structure of the BeF3-activated conformation of SdrG from Pseudomonas melonis Fr1
ComponentsSdrG
KeywordsPROTEIN / Single domain response regulator FAT GUY response regulator Allosteric transition General stress response
Function / homology
Function and homology information


phosphorelay signal transduction system
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
Biological speciesSphingomonas melonis Fr1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsCampagne, S. / Vorholt, J.A. / Allain, F.H.-T.
CitationJournal: Structure / Year: 2016
Title: Role of the PFXFATG[G/Y] Motif in the Activation of SdrG, a Response Regulator Involved in the Alphaproteobacterial General Stress Response.
Authors: Campagne, S. / Dintner, S. / Gottschlich, L. / Thibault, M. / Bortfeld-Miller, M. / Kaczmarczyk, A. / Francez-Charlot, A. / Allain, F.H. / Vorholt, J.A.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SdrG


Theoretical massNumber of molelcules
Total (without water)13,8931
Polymers13,8931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6710 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein SdrG


Mass: 13892.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas melonis Fr1 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C7D1A8*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D H
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D H(CCO)NH
161isotropic13D C(CO)NH
191isotropic23D 1H-15N NOESY
181isotropic23D 1H-13C NOESY aliphatic
171isotropic23D 1H-13C NOESY aromatic

-
Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] BeF3-activated conformation of SdrG, 10 mM sodium phosphate, 50 mM sodium chloride, 5 mM beryllium Chloride, 30 mM sodium fluoride, 10 mM magnesium chloride, 90% H2O/10% D2O
Label: 13C15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBeF3-activated conformation of SdrG[U-99% 13C; U-99% 15N]1
10 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
5 mMberyllium Chloridenatural abundance1
30 mMsodium fluoridenatural abundance1
10 mMmagnesium chloridenatural abundance1
Sample conditionsDetails: NaPO4 10 mM pH6.5 NaCl 50mM MgCl2 10mM NaF 30 mM BeCl2 5mM
Ionic strength: 105 mM / Label: 13C15N / pH: 6.5 / Pressure: AMBIENT Pa / Temperature: 293 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCEBrukerAVANCE9002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.96Bruker Biospincollection
CARA3.96Keller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / 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