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- PDB-1rau: SOLUTION STRUCTURE OF AN UNUSUALLY STABLE RNA TETRAPLEX CONTAININ... -

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Basic information

Entry
Database: PDB / ID: 1rau
TitleSOLUTION STRUCTURE OF AN UNUSUALLY STABLE RNA TETRAPLEX CONTAINING G-AND U-QUARTET STRUCTURES
ComponentsRNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
KeywordsRNA / TETRAPLEX
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR
AuthorsCheong, C. / Moore, P.B.
CitationJournal: Biochemistry / Year: 1992
Title: Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures.
Authors: Cheong, C. / Moore, P.B.
History
DepositionJul 29, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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 (5'-R(*UP*GP*GP*GP*GP*U)-3')
B: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
D: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)7,7934
Polymers7,7934
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 8
Representative

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Components

#1: RNA chain
RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')


Mass: 1948.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: RIBONUCLEIC ACID

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: ATA COLLECTION PARAMETERS: FREQUENCY: 500 MHZ FOR 1H, 202 MHZ FOR 31P SAMPLE TUBE: 5 MM SPECTRA FOR ASSIGNMENTS: HOMONUCLEAR PROTON 2D, 1H-31P COSY; SPECTRA FOR CONSTRAINTS: NOESY, DQF-COSY, 1H- ...Text: ATA COLLECTION PARAMETERS: FREQUENCY: 500 MHZ FOR 1H, 202 MHZ FOR 31P SAMPLE TUBE: 5 MM SPECTRA FOR ASSIGNMENTS: HOMONUCLEAR PROTON 2D, 1H-31P COSY; SPECTRA FOR CONSTRAINTS: NOESY, DQF-COSY, 1H-31P COSY MOLECULAR CHARACTERISTICS: OLIGOMER STATE: TETRAMERIC MOLECULAR WEIGHT: 13 KD NUCLEOTIDES: 24 SOLUTION CONDITIONS: SOLVENT: H2O AND 100% D2O TEMPERATURES: 5C AND 40C PH: 6.7 AND 5.2 STRAND CONCENTRATION: 2.2 MM ADDITIVES: 10 MM POTASSIUM PHOSPHATE, 50 MM KCL, 0.5 MM EDTA OR 18 MM POTASSIUM PHOSPHATE, 88 MM KCL, 0.9 MM EDTA

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Sample preparation

Details
Solution-IDSolvent system
1H2O AND 100% D2O
2H2O AND 100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMPOTASSIUM PHOSPHATE1
50 mMKCL1
.5 mMEDTA1
18 mMPOTASSIUM PHOSPHATE2
88 mMKCL2
.9 mMEDTA2
Sample conditions
Conditions-IDpHTemperature (K)
16.7 278 K
25.2 313 K

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementSoftware ordinal: 1
Details: STRUCTURE CALCULATION: MOLECULAR DYNAMICS AND ENERGY MINIMIZATION USING RELAXATION MATRIX ROUTINE IN X-PLOR CONSTRAINTS: TOTAL 428 DISTANCE CONSTRAINTS (ABOUT 18/NUCLEOTIDE) 212 FROM ...Details: STRUCTURE CALCULATION: MOLECULAR DYNAMICS AND ENERGY MINIMIZATION USING RELAXATION MATRIX ROUTINE IN X-PLOR CONSTRAINTS: TOTAL 428 DISTANCE CONSTRAINTS (ABOUT 18/NUCLEOTIDE) 212 FROM INTRANUCLEOTIDE NOES 112 FROM INTERNUCLEOTIDE NOES 36 FROM HYDROGEN BONDS 8 FROM EXCHANGEABLE PROTON NOES 60 DERIVED FROM BACKBONE TORSION ANGLES DIHEDRAL ANGLE CONSTRAINTS 104 BACKBONE AND GLYCOSIDIC TORSION ANGLES SUGAR RING TORSION ANGLES CONSTRAINTS TO MAKE QUARTET PLANES PLANAR 4-FOLD ROTATIONAL SYMMETRY CONSTRAINTS QUALITY OF STRUCTURE NUMBER OF REFINED STRUCTURES: 8 RMS DEVIATION: 0.71A FOR ALL HEAVY ATOMS
NMR constraintsNOE constraints total: 428 / NOE intraresidue total count: 212 / Hydrogen bond constraints total count: 36
NMR ensembleConformers calculated total number: 8 / Conformers submitted total number: 1

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