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- PDB-1xst: Solution structure of E.coli RNase P RNA P4 stem, U69A mutation, ... -

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Basic information

Entry
Database: PDB / ID: 1xst
TitleSolution structure of E.coli RNase P RNA P4 stem, U69A mutation, complexed with cobalt (III) hexammine.
ComponentsRNA (27-MER)
KeywordsRNA / Ribonuclease P RNA / Ribozyme / transfer RNA processing / P4 stem / U69A mutant / metal binding site / metal complex / cobalt (III) hexammine complex
Function / homologyCOBALT HEXAMMINE(III) / RNA / 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 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8172
Polymers8,6561
Non-polymers1611
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 RNA (27-MER) / RNase P RNA P4 stem


Mass: 8656.183 Da / Num. of mol.: 1 / Mutation: U69A / Source method: obtained synthetically
Details: enzymatically synthesized from DNA oligonucleotide template ny T7 RNA polymerase
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
2332D NOESY
142DQF-COSY
15231P-1H-HETERO-COSY
16231P-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. Intermolecular NOE crosspeaks between RNA ...Text: The structure was determined using standard 2D homonuclear techniques as well as 13C and 31P heteronuclear experiments performed at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and intermolecular distance constraints derived thereof were used to determine the site of cobalt (III) hexammine binding.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22mM P4 U69A RNA; 100mM NaCl; 10mM phosphate buffer; 100% D2O100% D2O
32mM P4 U69A RNA; 100mM NaCl; 6mM hexammine cobalt chloride; 10mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 6.4ambient 288 K
2100 mM NaCl, 6 mM Co(NH3)6Cl 6.4ambient 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: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.2Brukercollection
NMRPipe2.1F. Delaglioprocessing
X-PLOR3.1A. Bruengerstructure solution
X-PLOR3.1A. Bruengerrefinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: The average structure is based on the superposition of 14 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.85 Angstrom. A total of ...Details: The average structure is based on the superposition of 14 structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.85 Angstrom. A total of 290 NOE-derived distance constraints, 245 dihedral constraints and 48 distance constraints from hydrogen bonds were used in refinement. 15 NOE derived intermolecular distance constraints were used to localize the bound cobalt (III) hexammine.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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