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- PDB-1qpm: NMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1qpm
TitleNMR STRUCTURE OF THE MU BACTERIOPHAGE REPRESSOR DNA-BINDING DOMAIN
ComponentsPROTEIN (MU BACTERIOPHAGE C REPRESSOR PROTEIN)
KeywordsVIRAL PROTEIN / HELIX-TURN-HELIX / MU BACTERIOPHAGE / REPRESSOR
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
Biological speciesEnterobacteria phage Mu (virus)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
Model type detailsminimized average
AuthorsIlangovan, U. / Wojciak, J.M. / Connolly, K.M. / Clubb, R.T.
CitationJournal: Biochemistry / Year: 1999
Title: NMR structure and functional studies of the Mu repressor DNA-binding domain.
Authors: Ilangovan, U. / Wojciak, J.M. / Connolly, K.M. / Clubb, R.T.
History
DepositionMay 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 1999Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: 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
A: PROTEIN (MU BACTERIOPHAGE C REPRESSOR PROTEIN)


Theoretical massNumber of molelcules
Total (without water)7,5441
Polymers7,5441
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)26 / 50STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #26minimized average structure

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Components

#1: Protein PROTEIN (MU BACTERIOPHAGE C REPRESSOR PROTEIN)


Mass: 7543.704 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P06019

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE PRIMARY REFERENCE
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR METHODS. COMPLETE INFORMATION IN PRIMARY REFERENCE.

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Sample preparation

DetailsContents: 1MM REPRESSOR U-15N,13C 50MM PHOSPHATE (PH 6.2); 100MM NACL; 2.5MM D-DTT; 93% H2O, 7% D2O
Sample conditionsIonic strength: 100mM NACL / pH: 6.2 / Pressure: AMBIENT / Temperature: 300.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionClassification
X-PLOR3.843structure solution
X-PLOR3.843refinement
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1 / Details: INFORMATION IN PRIMARY REFERENCE
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 26

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