[English] 日本語
Yorodumi
- PDB-1qqi: SOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qqi
TitleSOLUTION STRUCTURE OF THE DNA-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI
ComponentsPHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
KeywordsTRANSCRIPTION / WINGED HELIX-TURN-HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / phosphorelay response regulator activity / DNA-binding transcription activator activity / regulation of DNA-templated transcription initiation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphate regulon transcriptional regulatory protein PhoB / Phosphate regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / 4D SIMULATED ANNEALING
AuthorsOkamura, H. / Hanaoka, S. / Nagadoi, A. / Makino, K. / Nishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box.
Authors: Okamura, H. / Hanaoka, S. / Nagadoi, A. / Makino, K. / Nishimura, Y.
History
DepositionJun 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Theoretical massNumber of molelcules
Total (without water)12,1741
Polymers12,1741
Non-polymers00
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 / -
Representative

-
Components

#1: Protein PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB


Mass: 12173.898 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PT7-7-CB / Production host: Escherichia coli (E. coli) / References: UniProt: P08402, UniProt: P0AFJ5*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D NOESY
1213D 13C-SEPARATED NOESY
1323D 15N-SEPARATED NOESY
1414D 13C-SEPARATED NOESY
152HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

-
Sample preparation

Details
Solution-IDContents
11-2MM PROTEIN U-15N,13C; 50MM PHOSPHATE BUFFER, 500MM NACL
21-2MM PROTEIN U-15N; 50MM PHOSPHATE BUFFER, 500MM NACL
31-2MM PROTEIN ; 50MM PHOSPHATE BUFFER, 500MM NACL
Sample conditionsIonic strength: NACL 500mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AMXBrukerAMX5002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.6DELAGLIO, F.structure solution
PIPP3.9GARRETT, D.S.structure solution
EMBOSS5NAKAI,T., KIDERA, A. AND NAKAMURA, H.refinement
RefinementMethod: 4D SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1758 RESTRAINTS, 1719 ARE NOE-DERIVED DISTANCE RESTRAINTS AND 39 DIHEDRAL ANGLE RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH EMBOSS BY USING ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1758 RESTRAINTS, 1719 ARE NOE-DERIVED DISTANCE RESTRAINTS AND 39 DIHEDRAL ANGLE RESTRAINTS. STRUCTURE CALCULATIONS WERE PERFORMED WITH EMBOSS BY USING A 4D SIMULATED ANNEALING PROTOCOL STARTING FROM A RANDOM COIL CONFORMATION. THE GENERATED STRUCTURES WERE FURTHER REFINED BY ENERGY MINIMIZATION USING THE AMBER FORCE FIELD. THE FINAL STRUCTURES WERE SELECTED BY HAVING NO DISTANCE VIOLATIONS GREATER THAN 0.3 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS GREATER THAN 5 DEGREES, AND A LOW TARGET ENERGY.
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