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- PDB-1eht: THEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, 10 ST... -

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Basic information

Entry
Database: PDB / ID: 1eht
TitleTHEOPHYLLINE-BINDING RNA IN COMPLEX WITH THEOPHYLLINE, NMR, 10 STRUCTURES
ComponentsTHEOPHYLLINE-BINDING RNA
KeywordsRNA / RIBONUCLEIC ACID
Function / homologyTHEOPHYLLINE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsZimmermann, G.R. / Pardi, A.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA.
Authors: Zimmermann, G.R. / Jenison, R.D. / Wick, C.L. / Simorre, J.P. / Pardi, A.
#1: Journal: Science / Year: 1994
Title: High-Resolution Molecular Discrimination by RNA
Authors: Jenison, R.D. / Gill, S.C. / Pardi, A. / Polisky, B.
History
DepositionMar 20, 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 1.3Feb 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
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: THEOPHYLLINE-BINDING RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8192
Polymers10,6381
Non-polymers1801
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 / 50LOWEST TOTAL ENERGY
Representative

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Components

#1: RNA chain THEOPHYLLINE-BINDING RNA


Mass: 10638.409 Da / Num. of mol.: 1 / Fragment: BINDING FRAGMENT, RESIDUES 1 - 33 / Source method: obtained synthetically
Details: CONSENSUS SEQUENCE OF THE THEOPHYLLINE BINDING RNA APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A THREE BASE-PAIR STEM, AND CAPPED BY A GAAA TETRALOOP
#2: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.8 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameVersionDeveloperClassification
X-PLORBRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 10

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