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- PDB-1am0: AMP RNA APTAMER COMPLEX, NMR, 8 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1am0
TitleAMP RNA APTAMER COMPLEX, NMR, 8 STRUCTURES
ComponentsRNA APTAMER
KeywordsRNA / COMPLEX (RIBONUCLEIC ACID-AMP) / RNA APTAMER / GNRA MOTIF / G(DOT)G MISMATCH / G(DOT)A MISMATCH / RIBONUCLEIC ACID
Function / homologyADENOSINE MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
AuthorsJiang, F. / Kumar, R.A. / Jones, R.A. / Patel, D.J.
Citation
Journal: Nature / Year: 1996
Title: Structural Basis of RNA Folding and Recognition in an AMP-RNA Aptamer Complex
Authors: Jiang, F. / Kumar, R.A. / Jones, R.A. / Patel, D.J.
#1: Journal: Nature / Year: 1994
Title: In Vitro Evolution of New Ribozymes with Polynucleotide Kinase Activity
Authors: Lorsch, J.R. / Szostak, J.W.
#2: Journal: Nature / Year: 1993
Title: An RNA Motif that Binds ATP
Authors: Sassanfar, M. / Szostak, J.W.
History
DepositionJun 19, 1997Processing site: BNL
SupersessionJul 23, 1997ID: 1ARA
Revision 1.0Jul 23, 1997Provider: 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA APTAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2932
Polymers12,9461
Non-polymers3471
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 8LEAST RESTRAINT VIOLATION
Representative

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Components

#1: RNA chain RNA APTAMER


Mass: 12945.754 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111IN D2O - NOESY
121COSY
131TOCSY
1412D (1)H-(31)P COSY
1512D(1)H-(13)C CT HSQC
1613D (1)H-(13)C-(1)H NOESY-HMQC
171(H)CCH-TOCSY
181(H)CCH-COSY. DISTANCE RESTRAINTS FROM 120 MS NOESY
191120 MS 3D NOESY-HMQC.

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Sample preparation

Sample conditions
Conditions-IDpHTemperature (K)
16.7 288 K
26.7 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS6001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR softwareName: X-PLOR 3.1F / Version: 3.1F / Developer: BRUNGER / Classification: refinement
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 8 / Conformers submitted total number: 8

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