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- PDB-2lqz: Structure of the RNA claw of the DNA packaging motor of bacteriop... -

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Basic information

Entry
Database: PDB / ID: 2lqz
TitleStructure of the RNA claw of the DNA packaging motor of bacteriophage 29
ComponentsRNA (27-MER)
KeywordsRNA / bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsHarjes, E.J. / Matsuo, H.J. / Kitamura, A.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structure of the RNA claw of the DNA packaging motor of bacteriophage 29.
Authors: Harjes, E. / Kitamura, A. / Zhao, W. / Morais, M.C. / Jardine, P.J. / Grimes, S. / Matsuo, H.
History
DepositionMar 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,5861
Polymers8,5861
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)9 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (27-MER)


Mass: 8586.128 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-1H NOESY
1212D 1H-15N HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1512D DQF-COSY

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Sample preparation

DetailsContents: 300 uM [U-100% 13C; U-100% 15N] RNA (27-MER), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: RNA (27-MER)-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA9003

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 12 / NA beta-angle constraints total count: 13 / NA chi-angle constraints total count: 12 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 12 / NA gamma-angle constraints total count: 13 / NA other-angle constraints total count: 29 / NA sugar pucker constraints total count: 99 / NOE constraints total: 429 / NOE intraresidue total count: 136 / NOE long range total count: 68 / NOE medium range total count: 33 / NOE sequential total count: 192
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 9

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