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- PDB-1nyb: SOLUTION STRUCTURE OF THE BACTERIOPHAGE PHI21 N PEPTIDE-BOXB RNA ... -

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Basic information

Entry
Database: PDB / ID: 1nyb
TitleSOLUTION STRUCTURE OF THE BACTERIOPHAGE PHI21 N PEPTIDE-BOXB RNA COMPLEX
Components
  • BoxB RNA
  • Probable regulatory protein N
KeywordsTRANSCRIPTION/RNA / peptide-rna complex / transcription antitermination / TRANSCRIPTION-RNA COMPLEX
Function / homologyDNA-templated transcription termination / RNA / RNA (> 10) / Probable regulatory protein N
Function and homology information
Biological speciesEnterobacteria phage phi21 (virus)
MethodSOLUTION NMR
Model type detailsminimized average
AuthorsCilley, C.D. / Williamson, J.R.
CitationJournal: RNA / Year: 2003
Title: Structural mimicry in the phage phi21 N peptide-boxB RNA complex
Authors: Cilley, C.D. / Williamson, J.R.
History
DepositionFeb 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 23, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: BoxB RNA
A: Probable regulatory protein N


Theoretical massNumber of molelcules
Total (without water)10,2462
Polymers10,2462
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)15 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain BoxB RNA


Mass: 7660.590 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesis of the RNA fragment from the Bacteriophage phi21 boxB
#2: Protein/peptide Probable regulatory protein N


Mass: 2584.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phi21 (virus) / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: P07243

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: The structure was determined using 2D homonuclear and 3D heteronuclear NMR spectroscopy. The two most important samples were uniformly labeled 15N,13C peptide or RNA in complex with its unlabeled counterpart.

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Sample preparation

DetailsContents: 2mM N peptide-boxB RNA complex; 25mM D6(98%)-succinate, 2mM NaCl, 0.2mM EDTA, 0.05mM Na-azide
Solvent system: 90% H20, 10% D2O
Sample conditionsIonic strength: 2mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX7502
Bruker AMXBrukerAMX6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Baxprocessing
NMRView4.1.3Bruce A. Johnsondata analysis
CNS1A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, G.L. Warrenrefinement
Amber6Case, D.A., Kollman, P.structure solution
RefinementSoftware ordinal: 1
Details: There were a total of 1016 distance restraints (including 48 hydrogen bond distance restraints) and 167 torsion restraints used to determine this structure. The molecular modeling of the ...Details: There were a total of 1016 distance restraints (including 48 hydrogen bond distance restraints) and 167 torsion restraints used to determine this structure. The molecular modeling of the phi21 N peptide-boxB RNA complex was done in three steps. First, a complete intramolecular restraint set was generated for each molecule, and then peptide and RNA structures were generated separately using ab initio simulated annealing (SA) starting from a random extended structure in CNSsolve. For both the peptide and the RNA, constrained (torsion) dynamics was used at 50000K. A total of 100 structures each of the peptide and RNA were generated. In the second step, each of the 20 lowest energy peptide and 20 lowest energy RNA structures were combined in single PDB files, in all 400 possible combinations. The RNA was held at the origin and the peptide was randomly rotated and moved 100 angstroms away in a random direction from the origin. These 400 possible "complexes" were docked using CNSsolve. The objective of the docking was to bring the peptide and RNA together without dramatically perturbing their folded structures from the first round of SA, so the temperatures for the docking were set much lower than in the initial calculations (1000 vs. 50000K). Finally, the 100 lowest energy docked structures were minimized by two rounds of low temperature annealing using Sander, a module of AMBER. As with the docking, the temperature was kept low (1000K). The 14 lowest energy structures were used for generating an average structure, which was energy minimized using a conjugate gradient.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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