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- PDB-1aw4: STRUCTURAL BASIS OF DNA FOLDING AND RECOGNITION IN AMP-DNA APTAME... -

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Basic information

Entry
Database: PDB / ID: 1aw4
TitleSTRUCTURAL BASIS OF DNA FOLDING AND RECOGNITION IN AMP-DNA APTAMER COMPLEX, NMR, 7 STRUCTURES
ComponentsATP-BINDING DNA APTAMER
KeywordsDNA / ADAPTIVE BINDING / AMP BINDING / DNA APTAMER / DNA BINDING / DNA RECOGNITION / AMP-DNA APTAMER COMPLEX
Function / homologyADENOSINE MONOPHOSPHATE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, DISTANCE RESTRAINED MD
AuthorsLin, C.H. / Patel, D.J.
CitationJournal: Chem.Biol. / Year: 1997
Title: Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.
Authors: Lin, C.H. / Patel, D.J.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: 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: ATP-BINDING DNA APTAMER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1973
Polymers8,5021
Non-polymers6942
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 21LEAST TOTAL ENERGY, NOE VIOLATION, VDW
Representative

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Components

#1: DNA chain ATP-BINDING DNA APTAMER


Mass: 8502.469 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / 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
111NOESY
121TOCSY
131COSY
1411H-13C HMQC

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Sample preparation

Sample conditionspH: 6.35 / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian VARIAN INOVA 600 / Manufacturer: Varian / Model: VARIAN INOVA 600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XVNMRstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, DISTANCE RESTRAINED MD / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST TOTAL ENERGY, NOE VIOLATION, VDW
Conformers calculated total number: 21 / Conformers submitted total number: 7

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