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- PDB-1cql: NMR STRUCTURE OF SRP RNA DOMAIN IV -

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Basic information

Entry
Database: PDB / ID: 1cql
TitleNMR STRUCTURE OF SRP RNA DOMAIN IV
ComponentsSRP DOMAIN IV RNA
KeywordsRNA / SRP / RNA STRUCTURE / DOMAIN IV / SIGNAL SEQUENCE RECOGNITION / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS RESTRAINED MOLECULAR DYNAMICS COMPLETE RELAXATION MATRIX ANALYSIS
AuthorsSchmitz, U. / James, T.L.
CitationJournal: RNA / Year: 1999
Title: Structure of the phylogenetically most conserved domain of SRP RNA.
Authors: Schmitz, U. / Behrens, S. / Freymann, D.M. / Keenan, R.J. / Lukavsky, P. / Walter, P. / James, T.L.
History
DepositionAug 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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: SRP DOMAIN IV RNA


Theoretical massNumber of molelcules
Total (without water)13,9631
Polymers13,9631
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 / 50structures with the least restraint violations in the crucial areas ot the molecule
Representative

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Components

#1: RNA chain SRP DOMAIN IV RNA


Mass: 13963.401 Da / Num. of mol.: 1 / Fragment: MODIFIED E. COLI SEQUENCE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
131DQF-COSY
141TOCSY
1513D (H)CCH-TOCSY
1613D (H)CCH-COSY
NMR detailsText: G- AND A-SINGLE NUCLEOTIDE ISOTOPE LABELED SAMPLES WERE USED BESIDES A UNIFORMLY LABELED RNA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25 - 1.2 mM RNA 10 mM potassium phoshpate 10 mM magnesium chloride pH 6.5D2O
20.25 mM RNA 10 mM potassium phoshpate 10 mM magnesium chloride pH 6.590% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5ambient 288 K
26.5ambient 303 K
36.5ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky92D.Kneller, T.Goddardstructure solution
MARDIGRAS92He Liu, B.Borgias, M.Tonellistructure solution
DYANA1.4P. Guentertrefinement
Amber4.1D.A. Pearlman et al.structure solution
Curves3R. Laverystructure solution
RefinementMethod: TORSION ANGLE DYNAMICS RESTRAINED MOLECULAR DYNAMICS COMPLETE RELAXATION MATRIX ANALYSIS
Software ordinal: 1 / Details: 16.4 DISTANCE RESTRAINTS/RESIDUE
NMR ensembleConformer selection criteria: structures with the least restraint violations in the crucial areas ot the molecule
Conformers calculated total number: 50 / Conformers submitted total number: 10

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