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- PDB-5uf3: Structure Effects of the Four-Adenine Loop of the Coliphage GA Re... -

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Basic information

Entry
Database: PDB / ID: 5uf3
TitleStructure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator
Componentsphage GA operator RNA hairpin
KeywordsRNA / phage / RNA hairpin / tetraloop / (A-A)-U motif
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEnterobacteria phage GA (virus)
MethodSOLUTION NMR
AuthorsChang, A.T. / Tran, M. / DeJong, E. / Nikonowicz, E.P.
CitationJournal: Biochemistry / Year: 2017
Title: Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator.
Authors: Chang, A.T. / Tran, M. / Nikonowicz, E.P.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 26, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: phage GA operator RNA hairpin


Theoretical massNumber of molelcules
Total (without water)7,3941
Polymers7,3941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / -
Representative

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Components

#1: RNA chain phage GA operator RNA hairpin


Mass: 7394.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage GA (virus)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-1H NOESY
121isotropic13D 1H-13C NOESY
131isotropic12D 1H-13C HSQC
141isotropic13D (H)CCH-TOCSY
253isotropic12D 1H-15N HSQC
165isotropic22D 1H-31P HETCOR
171isotropic22D 1H-13C CTEP
186isotropic12D 1H-13C HSQC
194anisotropic12D 1H-13C HSQC
2103isotropic13D 1H-15N NOESY
1111isotropic12D 1H-13C H(N)CO
1121isotropic12D 1H-15N HSQC
1131isotropic12D 1H-13C H(CN)CO
1141isotropic12D 1H-13C C(C)H-COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution11 mM [U-13C; U-15N] phage GA operator RNA hairpin, 10 mM potassium phosphate, 10 mM potassium chloride, 0.02 mM EDTA, 100% D2OphageGA_15N13C_D2O100% D2O
solution21.5 mM phage GA operator RNA hairpin, 10 mM potassium phosphate, 10 mM potassium chloride, 0.02 mM EDTA, 100% D2OphageGA_nl_D2O100% D2O
solution31 mM [U-13C; U-15N] phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM EDTA, 90% H2O/10% D2OphageGA_15N13C_H2O90% H2O/10% D2O
solution40.3 mM [U-13C; U-15N] phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 15 mg/mL Pf1 phage, 100% D2OphageGA_Pf1100% D2O
solution51.2 mM 2H, 40%-85% phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM EDTA, 100% D2OphageGA_fract_D100% D2Odeuteration achieved by culturing cells in 90% D2O and sodium acetate. See Nikonowicz, EP. Methods Enzymol. 338:320-341 (2001).
solution61.1 mM 13C, 4%-20% phage GA operator RNA hairpin, 10 mM potassium chloride, 10 mM potassium phosphate, 0.02 mM na EDTA, 100% D2OphageGA_fract_C100% D2OFractional 13-C enrichment achieved by culturing cells on 20% [13C-C2, 12C-C1], 80% [U-12C] sodium acetate. See Nikonowicz, EP. Methods Enzymol. 338:320-341 (2001).
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMphage GA operator RNA hairpin[U-13C; U-15N]1
10 mMpotassium phosphatenatural abundance1
10 mMpotassium chloridenatural abundance1
0.02 mMEDTAnatural abundance1
1.5 mMphage GA operator RNA hairpinnatural abundance2
10 mMpotassium phosphatenatural abundance2
10 mMpotassium chloridenatural abundance2
0.02 mMEDTAnatural abundance2
1 mMphage GA operator RNA hairpin[U-13C; U-15N]3
10 mMpotassium chloridenatural abundance3
10 mMpotassium phosphatenatural abundance3
0.02 mMEDTAnatural abundance3
0.3 mMphage GA operator RNA hairpin[U-13C; U-15N]4
10 mMpotassium chloridenatural abundance4
10 mMpotassium phosphatenatural abundance4
15 mg/mLPf1 phagenatural abundance4
1.2 mMphage GA operator RNA hairpin2H, 40%-85%5
10 mMpotassium chloridenatural abundance5
10 mMpotassium phosphatenatural abundance5
0.02 mMEDTAnatural abundance5
1.1 mMphage GA operator RNA hairpin13C, 4%-20%6
10 mMpotassium chloridenatural abundance6
10 mMpotassium phosphatenatural abundance6
0.02 mMEDTAna6
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1100% D2O20 mMcondition_16.8 pH*1 atm298 K
290% H2O, 10% D2O20 mMcondition_26.81 atm285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
FelixAccelrys Software Inc.processing
X-PLOR NIH2.43Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.43Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementSoftware ordinal: 5 / Details: RNA ff1 force field
NMR ensembleConformers submitted total number: 8

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