[English] 日本語
Yorodumi
- PDB-1p6q: NMR Structure of the Response regulator CheY2 from Sinorhizobium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p6q
TitleNMR Structure of the Response regulator CheY2 from Sinorhizobium meliloti, complexed with Mg++
ComponentsCheY2
KeywordsSIGNALING PROTEIN / CheY2 / Chemotaxis / Sinorhizobium meliloti / Signal transduction / Response regulator / Structural Proteomics in Europe / SPINE / Structural Genomics
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 speciesSinorhizobium meliloti (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsTOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1598, NUMBER OF INTRA-RESIDUE NOES USED FOR THE ...TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1598, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 796, NUMBER OF SEQUENTIAL NOES USED FOR THE CALCULATION: 437, NUMBER OF MEDIUM RANGE NOES USED FOR THE CALCULATION: 179, NUMBER OF LONG RANGE (I,J, J > I+4) NOES USED FOR THE CALCULATION: 186, NUMBER OF DIHEDRAL ANGLES RESTRAINTS USED FOR THE CALCULATION: 52, NUMBER OF HYDROGEN BOND RESTRAINTS USED FOR THE CALCULATION: 5, MINIMAL TARGET FUNCTION WAS 2.80, MEAN TARGET FUNCTION OF 16 STRUCTURES WAS 3.00 (+-0.4), THE NUMBER OF NOE VIOLATIONS > 0.02 NM WAS 3 (+-1), THE NUMBER OF NOE VIOLATIONS > 0.03 NM WAS 0, THE NUMBER OF DIHEDRAL ANGLES VIOLATIONS > 10 DEGREES WAS 0, RMSDS BACK BONE (6-124): 0.042 (+-0.015) NM, RMSDS ALL HEAVY ATOMS (6-124): 0.098 (+-0.016)NM
AuthorsRiepl, H. / Scharf, B. / Maurer, T. / Schmitt, R. / Kalbitzer, H.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution structures of the inactive and BeF3-activated response regulator CheY2.
Authors: Riepl, H. / Scharf, B. / Schmitt, R. / Kalbitzer, H.R. / Maurer, T.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CheY2


Theoretical massNumber of molelcules
Total (without water)13,7251
Polymers13,7251
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)16 / 250target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein CheY2


Mass: 13725.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q52884

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
171HNCA
181HNCO
191HN(CO)CA
1101CBCA(CO)CA
1111HBHA(CO)NH
1121(H)CCH-TOCSY
1131CC(CO)NH
NMR detailsText: TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1598, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 796, NUMBER OF SEQUENTIAL NOES USED FOR THE CALCULATION: 437, NUMBER OF MEDIUM RANGE ...Text: TOTAL NUMBER OF NOES USED FOR THE CALCULATION: 1598, NUMBER OF INTRA-RESIDUE NOES USED FOR THE CALCULATION: 796, NUMBER OF SEQUENTIAL NOES USED FOR THE CALCULATION: 437, NUMBER OF MEDIUM RANGE NOES USED FOR THE CALCULATION: 179, NUMBER OF LONG RANGE (I,J, J > I+4) NOES USED FOR THE CALCULATION: 186, NUMBER OF DIHEDRAL ANGLES RESTRAINTS USED FOR THE CALCULATION: 52, NUMBER OF HYDROGEN BOND RESTRAINTS USED FOR THE CALCULATION: 5, MINIMAL TARGET FUNCTION WAS 2.80, MEAN TARGET FUNCTION OF 16 STRUCTURES WAS 3.00 (+-0.4), THE NUMBER OF NOE VIOLATIONS > 0.02 NM WAS 3 (+-1), THE NUMBER OF NOE VIOLATIONS > 0.03 NM WAS 0, THE NUMBER OF DIHEDRAL ANGLES VIOLATIONS > 10 DEGREES WAS 0, RMSDS BACK BONE (6-124): 0.042 (+-0.015) NM, RMSDS ALL HEAVY ATOMS (6-124): 0.098 (+-0.016)NM

-
Sample preparation

DetailsContents: 1mM CheY2, 1MM TRIS-HCL, 5MM MGCL2 / Solvent system: 5mM MgCl2, 20mM Tris/HCl
Sample conditionspH: 6.83 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukerprocessing
AURELIA2.7.9Brukerdata analysis
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 250 / Conformers submitted total number: 16

+
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