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- PDB-2kvn: Phi29 E-loop hairpin -

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Basic information

Entry
Database: PDB / ID: 2kvn
TitlePhi29 E-loop hairpin
ComponentsRNA (5'-R(*GP*GP*UP*GP*AP*UP*UP*GP*AP*GP*UP*UP*CP*AP*CP*CP*A)-3')
KeywordsRNA / phi29 / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model type detailsminimized average
AuthorsHarris, S.M. / Schroeder, S.J.
CitationJournal: Biochemistry / Year: 2010
Title: Nuclear magnetic resonance structure of the prohead RNA E-loop hairpin.
Authors: Harris, S. / Schroeder, S.J.
History
DepositionMar 19, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _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
A: RNA (5'-R(*GP*GP*UP*GP*AP*UP*UP*GP*AP*GP*UP*UP*CP*AP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,4441
Polymers5,4441
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)30 / 132structures with no restraint violations
RepresentativeModel #1minimized average structure

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Components

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


Mass: 5444.269 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
1112D 1H-13C HSQC
2222D DQF-COSY
2322D 1H-1H NOESY
1412D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA, 10 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM sodium-EDTA, 100% D2O100% D2O
21 mM RNA, 10 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM sodium-EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMRNA1
10 mMsodium chloride1
10 mMsodium phosphate1
0.5 mMsodium-EDTA1
1 mMRNA2
10 mMsodium chloride2
10 mMsodium phosphate2
0.5 mMsodium-EDTA2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.5ambient 293 K
25.5ambient 274 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
SparkyGoddarddata analysis
SparkyGoddardprocessing
VNMRVariancollection
VNMRVariandata analysis
VNMRVarianprocessing
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmdata analysis
PyMOLDelanodata analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleAverage constraint violations per residue: 0 / Average constraints per residue: 15 / Average distance constraint violation: 0 Å / Average torsion angle constraint violation: 0 °
Conformer selection criteria: structures with no restraint violations
Conformers calculated total number: 132 / Conformers submitted total number: 30
Distance constraint violation method: cross validation, accept.inp script in CNS, only conformers with no violations were accepted
Maximum distance constraint violation: 0 Å / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å

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