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- PDB-2m12: Solution structure of the ID3 stem loop of domain 1 of the ai5gam... -

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Basic information

Entry
Database: PDB / ID: 2m12
TitleSolution structure of the ID3 stem loop of domain 1 of the ai5gamma group II intron
ComponentsRNA (5'-R(*GP*GP*GP*UP*GP*UP*AP*UP*UP*GP*GP*AP*AP*AP*UP*GP*AP*GP*CP*AP*CP*CP*C)-3')
KeywordsRNA / EBS1 / stem loop / ID3
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model3
AuthorsPopovic, M. / Greenbaum, N.L.
CitationJournal: Rna / Year: 2014
Title: Role of helical constraints of the EBS1-IBS1 duplex of a group II intron on demarcation of the 5' splice site.
Authors: Popovic, M. / Greenbaum, N.L.
History
DepositionNov 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*GP*UP*GP*UP*AP*UP*UP*GP*GP*AP*AP*AP*UP*GP*AP*GP*CP*AP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,4431
Polymers7,4431
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)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 7443.480 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: RNA stem loop
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-1H NOESY
2222D 1H-1H TOCSY
2322D DQF-COSY
1432D 1H-15N HSQC
2542D 1H-13C HSQC
2642D 1H-13C HSQC aliphatic
2742D 1H-13C HSQC aromatic
2833D 1H-15N NOESY
2943D (H)CCH-COSY
21043D (H)CCH-TOCSY
11112D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.03-0.9 mM ID3, 60 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.3-0.9 mM ID3, 60 mM sodium chloride, 100% D2O100% D2O
30.3-0.5 mM [U-100% 13C; U-100% 15N] ID3, 60 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
40.3-0.5 mM [U-100% 13C; U-100% 15N] ID3, 60 mM potassium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMID3-10.03-0.91
60 mMsodium chloride-21
mMID3-30.3-0.92
60 mMsodium chloride-42
mMID3-5[U-100% 13C; U-100% 15N]0.3-0.53
60 mMsodium chloride-63
mMID3-7[U-100% 13C; U-100% 15N]0.3-0.54
60 mMpotassium chloride-84
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.066.4ambient 277 K
20.066.4ambient 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CCPNCCPNchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 287 / NOE intraresidue total count: 130 / NOE long range total count: 26 / NOE sequential total count: 99
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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