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Basic information

Entry
Database: PDB / ID: 1u3k
TitleThe solution structure of a substrate of archaeal pre-tRNA splicing endonucleases
ComponentsABISS7
KeywordsRNA / bulge-helix-bulge
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Torsion angle dynamics, molecular dynamics
Model type detailsminimized average
AuthorsPollock, E.C. / Moore, P.B.
Citation
Journal: To be Published
Title: The solution structure of a substrate of archaeal pre-tRNA splicing endonucleases
Authors: Pollock, E.C. / Moore, P.B.
#1: Journal: Mol.Cell / Year: 1998
Title: Solution structure of a substrate for the archaeal pre-tRNA splicing endonucleases: the bulge-helix-bulge motif
Authors: Diener, J.L. / Moore, P.B.
History
DepositionJul 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: ABISS7


Theoretical massNumber of molelcules
Total (without water)12,3171
Polymers12,3171
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)10 / 65structures with acceptable covalent geometry, structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain ABISS7


Mass: 12317.423 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY-HSQC
121(H)CCH-COSY
131HSQC
141etc
NMR detailsText: This structure was determined with residual dipolar coupling data

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Sample preparation

DetailsContents: RNA molecule, 1-2mM in 80mM NaCl, 5mM phospate buffer pH 7, D2O
Solvent system: D2O
Sample conditionsIonic strength: 95mM / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, Adams, Clore, Delano, Gros, Gross-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenrefinement
Felix97Biosymprocessing
Sparky3Goddard and Knellerdata analysis
RefinementMethod: Torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations
Conformers calculated total number: 65 / Conformers submitted total number: 10

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