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- PDB-1xsg: Solution structure of E.coli RNase P RNA P4 stem oligoribonucleot... -

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Basic information

Entry
Database: PDB / ID: 1xsg
TitleSolution structure of E.coli RNase P RNA P4 stem oligoribonucleotide, U69A mutation
ComponentsRNase P RNA P4 stem
KeywordsRNA / Ribonuclease P RNA / Ribozyme / transfer RNA processing / P4 stem / U69A mutant / metal binding site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, simulated annealing
Model type detailsminimized average
AuthorsSchmitz, M.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy
Authors: Schmitz, M.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: 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 29, 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: RNase P RNA P4 stem


Theoretical massNumber of molelcules
Total (without water)8,6561
Polymers8,6561
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 / -
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNase P RNA P4 stem


Mass: 8656.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: enzymatically synthesized from DNA oligonucleotide template by T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
132DQF-COSY
14231P-1H-HETERO-COSY
15231P-1H-HETERO-TOCSY-NOESY
NMR detailsText: The structure was determined using standard 2D homonuclear techniques as well as 13C and 31P heteronuclear experiments performed at natural abundance

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
22mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer pH 6.4; 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.4 / Pressure: ambient / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.2Brukercollection
NMRPipe2.1F. Delaglioprocessing
X-PLOR3.1structure solution
X-PLOR3.1refinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: The average structure is based on the superposition of 12 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.78 Angstrom. A total of ...Details: The average structure is based on the superposition of 12 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.78 Angstrom. A total of 290 NOE-derived distance constraints, 245 dihedral restraints and 48 distance restraints from hydrogen bonds were used in refinement.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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