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- PDB-1raw: ATP BINDING RNA APTAMER IN COMPLEX WITH AMP, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1raw
TitleATP BINDING RNA APTAMER IN COMPLEX WITH AMP, NMR, 10 STRUCTURES
ComponentsRNA APTAMER
KeywordsRNA / RIBONUCLEIC ACID / UUCG TETRALOOP
Function / homologyADENOSINE MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsDieckmann, T. / Feigon, J.
Citation
Journal: RNA / Year: 1996
Title: Solution Structure of an ATP-Binding RNA Aptamer Reveals a Novel Fold
Authors: Dieckmann, T. / Suzuki, E. / Nakamura, G.K. / Feigon, J.
#1: Journal: Nature / Year: 1993
Title: An RNA Motif that Binds ATP
Authors: Sassanfar, M. / Szostak, J.W.
History
DepositionJul 17, 1996Processing site: BNL
Revision 1.0Jan 27, 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: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 APTAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0222
Polymers11,6751
Non-polymers3471
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 / 100LOWEST ENERGY STRUCTURES
Representative

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Components

#1: RNA chain RNA APTAMER / RAB


Mass: 11675.012 Da / Num. of mol.: 1 / Fragment: ATP-BINDING, RESIDUES 1 - 36 / Source method: obtained synthetically
Details: CONSENSUS SEQUENCE OF THE ATP BINDING RNA APTAMER FLANKED BY A 6 BASE PAIR STEM AND A FOUR BASE PAIR STEM CAPPED BY A UUCG TETRALOOP. COMPLEXED WITH AMP.
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX7502

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XPLOR3structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY STRUCTURES / Conformers calculated total number: 100 / Conformers submitted total number: 10

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