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- PDB-1f79: SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OL... -

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Entry
Database: PDB / ID: 1f79
TitleSOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM C70U MUTANT OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT(III) HEXAMMINE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsRNASE P RNA RIBOZYME, P4 DOMAIN MUTANT
KeywordsRNA / RIBONUCLEASE P / RIBOZYME / TRANSFER RNA PROCESSING / P4 STEM / C70U 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. / Tinoco Jr., I.
CitationJournal: RNA / Year: 2000
Title: Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
Authors: Schmitz, M. / Tinoco Jr., I.
History
DepositionJun 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7952
Polymers8,6341
Non-polymers1611
Water0
1


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

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Components

#1: RNA chain RNASE P RNA RIBOZYME, P4 DOMAIN MUTANT


Mass: 8634.127 Da / Num. of mol.: 1 / Fragment: P4 STEM / Mutation: C70U / Source method: obtained synthetically
Details: synthesized from DNA ologonucleotide template by 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
2222D NOESY
3332D NOESY
4442D NOESY
252DQF-COSY
26231P-1H-COSY
27213C-1H-HMQC
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Intermolecular NOE crosspeaks between RNA protons and ...Text: This structure was determined using standard 2D homonuclear techniques and 13C and 31P heteronuclear techniques at natural abundance. Intermolecular NOE crosspeaks between RNA protons and cobalt (III) hexammine protons and derived intermolecular distance constraints were used to determine the site of cobalt (III) hexammine binding in the complex structure

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22 mM P4m RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O99.96% D2O
32 mM P4m RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
42 mM P4m RNA; 100 mM sodium chloride; 3 mM hexammine cobalt chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM Na 6.5 ambient 288 K
2100 mM Na 6.5 ambient 288 K
3100 mM Na, 10 mM Mg 6.5 ambient 288 K
4100 mM Na, 3 mM Co(NH3)6 6.5 ambient 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
Felix95MSIprocessing
X-PLOR3.841Brungerstructure solution
X-PLOR3.841Brungerrefinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: The average structure is based on superposition of 12 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.5 Angstrom. A total ...Details: The average structure is based on superposition of 12 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.5 Angstrom. A total of 268 NOE-derived intramolecular distance constraints, 171 dihedral restraint and 49 distance restraints from hydrogen bonds were used in the refinement. 12 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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