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- PDB-1vop: CONSERVED RNA COMPONENT OF THE PEPTIDYL TRANSFERASE CENTER, NMR, ... -

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Basic information

Entry
Database: PDB / ID: 1vop
TitleCONSERVED RNA COMPONENT OF THE PEPTIDYL TRANSFERASE CENTER, NMR, 33 STRUCTURES
Components23S RIBOSOMAL RNA
KeywordsRNA / RIBOSOMAL RNA / HAIRPIN LOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsPuglisi, E.V. / Puglisi, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a conserved RNA component of the peptidyl transferase centre.
Authors: Puglisi, E.V. / Green, R. / Noller, H.F. / Puglisi, J.D.
History
DepositionAug 30, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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: 23S RIBOSOMAL RNA


Theoretical massNumber of molelcules
Total (without water)4,2291
Polymers4,2291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)33 / 100LOWEST ENERGY
Representative

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Components

#1: RNA chain 23S RIBOSOMAL RNA /


Mass: 4228.565 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDES 2247 - 2256 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: 10MM NA PHOSPHATE

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Sample preparation

Sample conditionspH: 6.4 / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
Discoverstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 33

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