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- PDB-1g4d: NMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAI... -

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Basic information

Entry
Database: PDB / ID: 1g4d
TitleNMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN/DNA COMPLEX
Components
  • 5'-D(P*CP*AP*GP*AP*TP*TP*AP*CP*TP*GP*AP*AP*AP*AP*GP*G)-3'
  • 5'-D(P*CP*CP*TP*TP*TP*TP*CP*AP*GP*TP*AP*AP*TP*CP*TP*G)-3'
  • REPRESSOR PROTEIN C
KeywordsViral protein/DNA / protein-DNA complex / helix-turn-helix / winged-helix / bacteriophage Mu / repressor / virus/viral protein / Viral protein-DNA COMPLEX
Function / homology
Function and homology information


viral latency / latency-replication decision / transcription repressor complex / host cell cytoplasm / DNA binding
Similarity search - Function
Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. / Putative DNA-binding domain 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
DNA / DNA (> 10) / Repressor protein c
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsWojciak, J.M. / Iwahara, J. / Clubb, R.T.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove.
Authors: Wojciak, J.M. / Iwahara, J. / Clubb, R.T.
History
DepositionOct 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(P*CP*CP*TP*TP*TP*TP*CP*AP*GP*TP*AP*AP*TP*CP*TP*G)-3'
C: 5'-D(P*CP*AP*GP*AP*TP*TP*AP*CP*TP*GP*AP*AP*AP*AP*GP*G)-3'
A: REPRESSOR PROTEIN C


Theoretical massNumber of molelcules
Total (without water)17,3383
Polymers17,3383
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)25 / -structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4839.151 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*CP*AP*GP*AP*TP*TP*AP*CP*TP*GP*AP*AP*AP*AP*GP*G)-3'


Mass: 4955.256 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein REPRESSOR PROTEIN C / / MU BACTERIOPHAGE C REPRESSOR PROTEIN


Mass: 7543.704 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DNA-BINDING DOMAIN (RESIDUES 13-81)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / Gene: MU C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06019

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM complex: U-15N protein, unlabeled DNA; 25mM PO490% H2O/10% D2O
21mM complex: U-15N,13C protein, unlabeled DNA; 25mM PO490% H2O/10% D2O
31mM complex: U-15N,13C protein, unlabeled DNA; 25mM PO4100% D2O
41mM complex: unlabeled protein, U-15N,13C DNA; 25mM PO490% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.2 1 atm305 K
26.2 1 atm305 K
36.2 1 atm305 K
46.2 1 amt305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameClassification
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers submitted total number: 25

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