[English] 日本語
Yorodumi
- PDB-1j56: MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC REC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j56
TitleMINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE SITE CONTACTS
ComponentsNITROGEN REGULATION PROTEIN NR(I)
KeywordsSIGNALING PROTEIN / two component signal transduction / receiver domain / BeF3 / phosphorylation / Bacterial nitrogen regulatory protein
Function / homology
Function and homology information


regulation of nitrogen utilization / nitrogen fixation / phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / positive regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
DNA-binding transcriptional regulator NtrC / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain ...DNA-binding transcriptional regulator NtrC / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / DNA-binding transcriptional regulator NtrC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, simulated annealing, ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsHastings, C.A. / Lee, S.-Y. / Cho, H.S. / Yan, D. / Kustu, S. / Wemmer, D.E.
Citation
Journal: Biochemistry / Year: 2003
Title: High-Resolution Solution Structure of the Beryllofluoride-Activated NtrC Receiver Domain
Authors: Hastings, C.A. / Lee, S.-Y. / Cho, H.S. / Yan, D. / Kustu, S. / Wemmer, D.E.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: NMR STRUCTURE OF ACTIVATED CHEY
Authors: Cho, H.S. / Lee, S.-Y. / Yan, D. / Pan, X. / Parkinson, J.S. / Kustu, S. / Wemmer, D.E. / Pelton, J.G.
#2: Journal: Nat.Struct.Biol. / Year: 2001
Title: CRYSTAL STRUCTURE OF AN ACTIVATED RESPONSE REGULATOR BOUND TO ITS TARGET
Authors: Lee, S.-Y. / Cho, H.S. / Pelton, J.G. / Yan, D. / Henderson, R.K. / King, D.S. / Huang, L. / Kustu, S. / Berry, E.A. / Wemmer, D.E.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NITROGEN REGULATION PROTEIN NR(I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7032
Polymers13,6371
Non-polymers661
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

-
Components

#1: Protein NITROGEN REGULATION PROTEIN NR(I)


Mass: 13636.604 Da / Num. of mol.: 1
Fragment: N-terminal domain: Receiver domain, Residues 1-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P41789
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2224D 13C/15N-separated NOESY
2324D 13C-separated NOESY
2423D 13C-separated NOESY
252HNCA-J
262CBCA(CO)NH
37313C,1H-HSQC
484IPAP-HSQC
292HNHA
NMR detailsText: MINIMIZED AVERAGE STRUCTURE OF BERYLLOFLUORIDE-ACTIVATED NTRC RECEIVER DOMAIN: MODEL STRUCTURE INCORPORATING ACTIVE 3 SITE CONTACTS.

-
Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N; 1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O95% H2O/5% D2O
2U-15N, 13C;1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O95% H2O/5% D2O
310% 13C;1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O95% H2O/5% D2O
4U-15N; 1.1-1.5mM NtrC receiver domain(1-124); 50mM sodium phosphate buffer(pH6.75); 50mM NaCl; 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF; 95% H2O, 5% D2O; 30mg/ml phage pf195% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75ambient 303 K
250mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75ambient 303 K
350mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75ambient 303 K
450mM NaCl, 4.4mM BeCl2, 7.2mM MgCl2, 29mM NaF 6.75ambient 303 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 AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntertstructure solution
CNS 1.0Brungerstructure solution
Felixprocessing
NMRViewJohnsondata analysis
CNS 1.0Brunger et. al.refinement
MOLMOLrefinement
RefinementMethod: distance geometry, torsion angle dynamics, simulated annealing, ENERGY MINIMIZATION
Software ordinal: 1
Details: 3 additional constraints from crystal structure of BeF3-activated CheY were used for structure calculation.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

+
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