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- PDB-1e4p: Structure of the ribozyme substrate hairpin of Neurospora VS RNA.... -

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Basic information

Entry
Database: PDB / ID: 1e4p
TitleStructure of the ribozyme substrate hairpin of Neurospora VS RNA. A close look at the cleavage site
ComponentsRNA (5'-R(*GP*UP*GP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP* AP*GP*UP*CP*CP*GP*AP*GP*CP*GP*C)-3')
KeywordsRNA RIBOZYME / SUBSTRATE HAIRPIN
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNEUROSPORA SP. (fungus)
MethodSOLUTION NMR / TORSIAN ANGLE DYNAMICS
AuthorsMichiels, P.J.A. / Schouten, C.H.J. / Heus, H.A. / Hilbers, C.W.
CitationJournal: RNA / Year: 2000
Title: Structure of the Ribozyme Substrate Hairpin of Neurospora Vs RNA: A Close Look at the Cleavage Site
Authors: Michiels, P.J.A. / Schouten, C.H.J. / Hilbers, C.W. / Heus, H.A.
History
DepositionJul 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,8101
Polymers7,8101
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 / 100LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
RepresentativeModel #1

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Components

#1: RNA chain RNA (5'-R(*GP*UP*GP*CP*GP*AP*AP*GP*AP*CP*GP*AP*AP* AP*GP*UP*CP*CP*GP*AP*GP*CP*GP*C)-3') / NEUROSPORA VS RNA SUBSTRATE HAIRPIN


Mass: 7809.759 Da / Num. of mol.: 1 / Fragment: SUBSTRATE HAIRPIN / Mutation: YES / Source method: obtained synthetically / Source: (synth.) NEUROSPORA SP. (fungus)
Compound detailsU617G, G643C, STEM-LOOP IB (G625-C635) IS REPLACED BY R(ACGAAAGU)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
1411H-31P HETCOR
1511H-13C HMQC
1611H-31P HETERO-TOCSY-NOESY
171NOESY-J

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Sample preparation

Sample conditionsIonic strength: 100 mM / pH: 5 / Temperature: 302 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: TORSIAN ANGLE DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST ENERGY
Conformers calculated total number: 100 / Conformers submitted total number: 20

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