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- PDB-1f6x: SOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM OLIGORIBON... -

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Basic information

Entry
Database: PDB / ID: 1f6x
TitleSOLUTION STRUCTURE OF THE RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE
ComponentsRNASE P RNA RIBOZYME, P4 DOMAIN
KeywordsRNA / RIBONUCLEASE P / RIBOZYME / TRANSFER RNA PROCESSING / P4 STEM / METAL BINDING SITE
Function / homologyRNA / 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
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: RNASE P RNA RIBOZYME, P4 DOMAIN


Theoretical massNumber of molelcules
Total (without water)8,6331
Polymers8,6331
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 RIBOZYME, P4 DOMAIN


Mass: 8633.143 Da / Num. of mol.: 1 / Fragment: P4 STEM / Source method: obtained synthetically
Details: 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
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

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
22 mM P4 RNA; 100 mM sodium chloride; 10 mM phosphate buffer; 99.96% D2O99.96% D2O
32 mM P4 RNA; 100 mM sodium chloride; 10 mM magnesium chloride; 10 mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
42 mM P4 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 6.5ambient 288 K
2100 mM Na 6.5ambient 288 K
3100 mM Na, 10 mM Mg 6.5ambient 288 K
4100 mM Na, 3 mM Co(NH3)6 6.5ambient 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 nine converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.8 Angstrom. A ...Details: The average structure is based on superposition of nine converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.8 Angstrom. A total of 266 NOE-derived distance constraints, 164 dihedral restraints and 48 distance restraints from hydrogen bonds were used in the refinement
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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