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- PDB-2m57: NMR solution structure of domain 5 from Azotobacter vinelandii In... -

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Basic information

Entry
Database: PDB / ID: 2m57
TitleNMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8
ComponentsRNA_(35-MER)
KeywordsRNA / ribozyme / group II intron / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsPechlaner, M. / Donghi, D. / Zelenay, V. / Sigel, R.K.O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron.
Authors: Pechlaner, M. / Donghi, D. / Zelenay, V. / Sigel, R.K.
History
DepositionFeb 15, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA_(35-MER)


Theoretical massNumber of molelcules
Total (without water)11,2691
Polymers11,2691
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA_(35-MER)


Mass: 11268.708 Da / Num. of mol.: 1 / Fragment: group II intron Domain 5 (D5) / Source method: obtained synthetically
Details: the sequence occurs naturally as part of Intron 5 from A.vinelandii and was transcribed in vitro using T7 RNA polymerase from a dsDNA template
Source: (synth.) Azotobacter vinelandii (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1252D 1H-1H NOESY
2322D 1H-1H NOESY
1412D 1H-1H TOCSY
2542D 1H-15N HSQC
1632D 1H-13C HSQC aromatic
1732D 1H-13C HSQC aliphatic
2842D JNN HNN COSY
3912D 1H-1H NOESY
41012D 1H-1H NOESY
51122D 1H-1H NOESY
61222D 1H-1H NOESY
31332D 1H-13C HSQC aromatic
41432D 1H-13C HSQC aromatic
41532D 1H-13C HSQC aliphatic
51642D 1H-15N HSQC
61742D 1H-15N HSQC
51842D JNN HNN COSY
61942D JNN HNN COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.5-1 mM RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1 mM [100% 13C; 100% 15N] RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
40.5-1 mM [100% 13C; 100% 15N] RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
50.5-1 mM [3',4',5',5'',5]-100% 2D RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (35-MER)-10.5-11
60 mMpotassium chloride-21
10 uMEDTA-31
mMRNA (35-MER)-40.5-12
60 mMpotassium chloride-52
10 uMEDTA-62
mMRNA (35-MER)-7[100% 13C; 100% 15N]0.5-13
60 mMpotassium chloride-83
10 uMEDTA-93
mMRNA (35-MER)-10[100% 13C; 100% 15N]0.5-14
60 mMpotassium chloride-114
10 uMEDTA-124
mMRNA (35-MER)-13[3',4',5',5'',5]-100% 2D0.5-15
60 mMpotassium chloride-145
10 uMEDTA-155
Sample conditions
Conditions-IDIonic strengthPressure (kPa)Temperature (K)pH
160ambient 300 K
260ambient 275 K7.8
560ambient 275 K5.2
660ambient 275 K6.7

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
TopSpin3.0.aBruker Biospinprocessing
TopSpin3.0.aBruker Biospindata analysis
CurvesLaverydata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 660 / NOE intraresidue total count: 238 / NOE long range total count: 98 / NOE medium range total count: 14 / NOE sequential total count: 310 / Hydrogen bond constraints total count: 56
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.2 Å

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