[English] 日本語
Yorodumi
- PDB-2xdi: Tryptophan repressor with L75F mutation in its apo form (no L- tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xdi
TitleTryptophan repressor with L75F mutation in its apo form (no L- tryptophan bound)
ComponentsTRP OPERON REPRESSOR
KeywordsTRANSCRIPTION / APO-L75F-TRPR / L-TRP BINDING
Function / homology
Function and homology information


sequence-specific DNA binding / nucleic acid binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
TrpR-like / Trp repressor, bacterial / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Trp operon repressor
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / CNS-XPLOR
AuthorsTyler, R. / Copie, V.
CitationJournal: Biochemistry / Year: 2002
Title: Three-Dimensional Solution NMR Structure of Apo-L75F-Trpr, a Temperature-Sensitive Mutant of the Tryptophan Repressor Protein.
Authors: Tyler, R. / Pelczer, I. / Carey, J. / Copie, V.
History
DepositionMay 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Atomic model / Database references ...Atomic model / Database references / Other / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRP OPERON REPRESSOR
B: TRP OPERON REPRESSOR


Theoretical massNumber of molelcules
Total (without water)24,5462
Polymers24,5462
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein TRP OPERON REPRESSOR


Mass: 12272.950 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TEMPERATURE SENSITIVE MUTANT DNA-BINDING PROTEIN / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PJPR2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CY15075 / References: UniProt: P0A882

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
121HN(CA)CB
131CBCA(CO) NH
141C(CO)NH
151HBHA(CO)NH
161HC(CO)NH
1711H NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED APO-L75F-TRPR

-
Sample preparation

DetailsContents: 500 MM NACL, 50 MM NAH2PO4, AND 90% H2O/10% D2O PH 5.7
Sample conditionspH: 5.7 / Temperature: 318.0 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
RefinementMethod: CNS-XPLOR / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE 20 MODELS IN THE DEPOSITED CO-ORDINATE FILE HAVE SUPERIMPOSED C-ALPHA TRACES OF ONLY THE SECONDARY STRUCTURE FORMING RESIDUES. ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE 20 MODELS IN THE DEPOSITED CO-ORDINATE FILE HAVE SUPERIMPOSED C-ALPHA TRACES OF ONLY THE SECONDARY STRUCTURE FORMING RESIDUES. THIS IS BECAUSE IT IS MORE INFORMATIVE TO ALIGN ONLY THE STABLE SEGMENTS THAN COMPLETE BACKBONES OF APO-L75F-TRPR PROTEIN DUE TO ITS FLEXIBLE NATURE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 40 / 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