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- PDB-17ra: BRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 CO... -

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Basic information

Entry
Database: PDB / ID: 17ra
TitleBRANCHPOINT HELIX FROM YEAST AND BINDING SITE FOR PHAGE GA/MS2 COAT PROTEINS, NMR, 12 STRUCTURES
ComponentsRNA
KeywordsRNA / BRANCHPOINT HELIX / PHAGE MS2 / BULGE / BASE TRIPLE / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsNikonowicz, E.P. / Smith, J.S.
CitationJournal: Biochemistry / Year: 1998
Title: NMR structure and dynamics of an RNA motif common to the spliceosome branch-point helix and the RNA-binding site for phage GA coat protein.
Authors: Smith, J.S. / Nikonowicz, E.P.
History
DepositionAug 4, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA


Theoretical massNumber of molelcules
Total (without water)6,7291
Polymers6,7291
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)12 / 75LEAST RESTRAINT VIOLATION
Representative

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Components

#1: RNA chain RNA


Mass: 6729.044 Da / Num. of mol.: 1 / Fragment: RBS AND START SITE FOR PHAGE GA REPLICASE GENE / Mutation: A5U, A6U / Source method: obtained synthetically
Details: IN VITRO SYNTHESIS FROM DNA TEMPLATE USING T7 RNA POLYMERASE. HAIRPIN CORRESPONDS TO NT -16 - +5 OF PHAGE GA REPLICASE AND THE YEAST PRE-MRNA BRANCHPOINT HELIX

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D/3D NOESY
121COSY
131HETCOR
NMR detailsText: FURTHER DETAILS OF DATA ACQUISITION AND STRUCTURE CALCULATION CAN BE FOUND IN THE METHODS SECTION OF THE MANUSCRIPT LISTED ABOVE. MODELS 1-6 ARE MINIMIZED STRUCTURES CALCULATED WITHOUT BASE ...Text: FURTHER DETAILS OF DATA ACQUISITION AND STRUCTURE CALCULATION CAN BE FOUND IN THE METHODS SECTION OF THE MANUSCRIPT LISTED ABOVE. MODELS 1-6 ARE MINIMIZED STRUCTURES CALCULATED WITHOUT BASE PAIR CONSTRAINTS FOR A6, A7, AND U16. MODELS 7-12 ARE MINIMIZED STRUCTURES CALCULATED USING A6-U16 BASE PAIR CONSTRAINTS AND AN A7 N1H-U16 O2 HYDROGEN BOND.

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Sample preparation

DetailsContents: 10% H2O/90% D2O, 100% D2O
Sample conditionsIonic strength: 20 mM / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felix950structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 75 / Conformers submitted total number: 12

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