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- PDB-1hji: BACTERIOPHAGE HK022 NUN-PROTEIN-NUTBOXB-RNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1hji
TitleBACTERIOPHAGE HK022 NUN-PROTEIN-NUTBOXB-RNA COMPLEX
Components
  • NUN-PROTEIN
  • RNA (5-R(P*GP*CP*CP*CP*UP*GP*AP*AP*AP*AP*AP*GP*GP*GP*C)-3)
KeywordsBACTERIOPHAGE HK022 / TERMINATION / PEPTIDE-RNA-COMPLEX / PEPTIDE-RNA-RECOGNITION / PROTEIN/RNA
Function / homologynegative regulation of DNA-templated transcription, elongation / DNA-templated transcription termination / RNA / RNA (> 10) / Transcription termination factor nun
Function and homology information
Biological speciesBACTERIOPHAGE LAMBDA (virus)
BACTERIOPHAGE HK022 (virus)
MethodSOLUTION NMR / molecular dynamics
AuthorsFaber, C. / Schaerpf, M. / Becker, T. / Sticht, H. / Roesch, P.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The Structure of the Coliphage Hk022 Nun Protein-Lambda-Phage Boxb RNA Complex. Implications for the Mechanism of Transcription Termination
Authors: Faber, C. / Schaerpf, M. / Becker, T. / Sticht, H. / Roesch, P.
#1: Journal: Eur.J.Biochem. / Year: 2000
Title: Antitermination in Bacteriophage Lambda: The Structure of the N36 Peptide-Boxb RNA Complex
Authors: Schaerpf, M. / Sticht, H. / Schweimer, K. / Boehm, M. / Hoffmann, S. / Roesch, P.
History
DepositionJan 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Structure summary / Category: pdbx_nmr_representative / Item: _pdbx_nmr_representative.conformer_id
Revision 1.4May 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5-R(P*GP*CP*CP*CP*UP*GP*AP*AP*AP*AP*AP*GP*GP*GP*C)-3)
B: NUN-PROTEIN


Theoretical massNumber of molelcules
Total (without water)8,0222
Polymers8,0222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 120LOWEST ENERGY
RepresentativeModel #1

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Components

#1: RNA chain RNA (5-R(P*GP*CP*CP*CP*UP*GP*AP*AP*AP*AP*AP*GP*GP*GP*C)-3)


Mass: 4853.994 Da / Num. of mol.: 1 / Fragment: BACTERIOPHAGE LAMBDA NUTBOXB-RNA
Source method: isolated from a genetically manipulated source
Details: NUTBOXB-RNA FROM THE NUTR-SEQUENCE / Source: (gene. exp.) BACTERIOPHAGE LAMBDA (virus) / Production host: ESCHERICHIA COLI (E. coli)
#2: Protein/peptide NUN-PROTEIN


Mass: 3167.657 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BINDING-DOMAIN, RESIDUES 19-44 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE HK022 (virus) / References: UniProt: P18683

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY

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Sample preparation

Sample conditionsIonic strength: 90 mM / pH: 6.5 / Pressure: 1 atm / Temperature: 301.0 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NDEEstructure solution
X-PLORstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 120 / Conformers submitted total number: 20

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