[English] 日本語
Yorodumi
- PDB-1rcs: NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rcs
TitleNMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX
Components
  • DNA (5'-D(*CP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*AP*CP*G)-3')
  • TRP REPRESSOR
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION REGULATION / REPRESSOR / DNA-BINDING / TRP / DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / 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
TRYPTOPHAN / DNA / DNA (> 10) / Trp operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsZhao, D. / Zheng, Z.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The solution structures of the trp repressor-operator DNA complex.
Authors: Zhang, H. / Zhao, D. / Revington, M. / Lee, W. / Jia, X. / Arrowsmith, C. / Jardetzky, O.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Solution Structures of the Escherichia Coli Trp Holo-and Aporepressor
Authors: Zhao, D. / Arrowsmith, C.H. / Jia, X. / Jardetzky, O.
#2: Journal: J.Phys.Chem. / Year: 1993
Title: Sequential Simulated Annealing: An Efficient Procedure for Structural Refinement Based on NMR Constraints
Authors: Zhao, D. / Jardetzky, O.
#3: Journal: Eur.J.Biochem. / Year: 1991
Title: The Solution Structures of Escherichia Coli Trp Repressor and Trp Aporepressor at an Intermediate Resolution
Authors: Arrowsmith, C. / Pachter, R. / Altman, R. / Jardetzky, O.
#4: Journal: Biochemistry / Year: 1990
Title: Sequence-Specific 1H NMR Assignments and Secondary Structure in Solution of Escherichia Coli Trp Repressor
Authors: Arrowsmith, C.H. / Pachter, R. / Altman, R.B. / Iyer, S.B. / Jardetzky, O.
#5: Journal: Biochemistry / Year: 1989
Title: NMR Assignments for the Amino-Terminal Residues of Trp Repressor and Their Role in DNA Binding
Authors: Arrowsmith, C.H. / Carey, J. / Treat-Clemons, L. / Jardetzky, O.
History
DepositionMay 12, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
E: DNA (5'-D(*CP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*AP*CP*G)-3')
F: DNA (5'-D(*CP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*AP*CP*G)-3')
A: TRP REPRESSOR
B: TRP REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7546
Polymers36,3454
Non-polymers4082
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / -
Representative

-
Components

#1: DNA chain DNA (5'-D(*CP*GP*TP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*AP*CP*G)-3')


Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein TRP REPRESSOR


Mass: 12039.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: CY15070 AND CY17071 / References: UniProt: P0A881
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 15

+
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