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- PDB-1co0: NMR STUDY OF TRP REPRESSOR-MTR OPERATOR DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1co0
TitleNMR STUDY OF TRP REPRESSOR-MTR OPERATOR DNA COMPLEX
Components
  • 5'-D(*TP*GP*TP*AP*CP*CP*AP*GP*TP*AP*CP*AP*CP*GP*AP*GP*TP*AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*AP*CP*TP*CP*GP*TP*GP*TP*AP*CP*TP*GP*GP*TP*AP*CP*A)-3'
  • TRP OPERON REPRESSOR
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / REPRESSOR / DNA-BINDING / TRP / DNA
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
AuthorsZhou, G.P. / Brocchieri, L. / Jardetzky, O.
Citation
Journal: Structures and Mechanisms, ACS Symposium Series / Year: 2002
Title: Allostery and Induced Fit, NMR and Molecular Modeling Study of the trp-repressor - mtr DNA complex
Authors: Brocchieri, L. / Zhou, G.P. / Jardetzky, O.
#1: 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.
#2: 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.
History
DepositionMay 30, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 5'-D(*TP*GP*TP*AP*CP*TP*CP*GP*TP*GP*TP*AP*CP*TP*GP*GP*TP*AP*CP*A)-3'
F: 5'-D(*TP*GP*TP*AP*CP*CP*AP*GP*TP*AP*CP*AP*CP*GP*AP*GP*TP*AP*CP*A)-3'
A: TRP OPERON REPRESSOR
B: TRP OPERON REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1536
Polymers36,7454
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 / 30LEAST RESTRAINT VIOLATION
Representative

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Components

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


Mass: 6139.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRP OPERON SEQUENCE FROM ESCHERICHIA COLI
#2: DNA chain 5'-D(*TP*GP*TP*AP*CP*CP*AP*GP*TP*AP*CP*AP*CP*GP*AP*GP*TP*AP*CP*A)-3'


Mass: 6126.994 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRP OPERON SEQUENCE FROM ESCHERICHIA COLI
#3: Protein TRP OPERON REPRESSOR


Mass: 12238.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / Strain (production host): CY15070,CY17071 / References: UniProt: P0A881
#4: Chemical ChemComp-TRP / TRYPTOPHAN


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 5.7 / Temperature units: K

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 30 / Conformers submitted total number: 15

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