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- PDB-1bn0: SL3 HAIRPIN FROM THE PACKAGING SIGNAL OF HIV-1, NMR, 11 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bn0
TitleSL3 HAIRPIN FROM THE PACKAGING SIGNAL OF HIV-1, NMR, 11 STRUCTURES
ComponentsSL3 RNA HAIRPIN
KeywordsRNA / HIV-1 / PACKAGING / TETRALOOP / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
AuthorsPappalardo, L. / Kerwood, D.J. / Pelczer, I. / Borer, P.N.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Three-dimensional folding of an RNA hairpin required for packaging HIV-1.
Authors: Pappalardo, L. / Kerwood, D.J. / Pelczer, I. / Borer, P.N.
History
DepositionJul 31, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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: SL3 RNA HAIRPIN


Theoretical massNumber of molelcules
Total (without water)6,4781
Polymers6,4781
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)11 / 500LEAST RESTRAINT VIOLATION
Representative

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Components

#1: RNA chain SL3 RNA HAIRPIN


Mass: 6477.919 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131H-PCOSY
NMR detailsText: THE STRUCTURES WERE DETERMINED FROM 2D NOESY EXPERIMENTS PERFORMED BOTH IN H2O AND D2O. THE DISTANCE RESTRAINTS DETERMINED FROM MARDIGRAS WERE BASED ON INTENSITIES FROM A NOESY WITH A MIXING ...Text: THE STRUCTURES WERE DETERMINED FROM 2D NOESY EXPERIMENTS PERFORMED BOTH IN H2O AND D2O. THE DISTANCE RESTRAINTS DETERMINED FROM MARDIGRAS WERE BASED ON INTENSITIES FROM A NOESY WITH A MIXING TIME OF 300MS. DQF-COSY AND H-P COSY WERE USED TO ASCERTAIN INFORMATION ABOUT THE TORSION ANGLES.

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Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: 30mM / pH: 7 / Pressure: NORMAL / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX500 / Manufacturer: Bruker / Model: DRX500 / Field strength: 500 MHz

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
MARDIGRASstructure solution
DYANAstructure solution
Amberstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: AVERAGE SIXTH ROOT RESIDUAL NMR INDEX = 0.07, AVERAGE RESTRAINT VIOLATION = 0.06 ANGSTROM.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 500 / Conformers submitted total number: 11

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