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- PDB-1f78: SOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLE... -

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Basic information

Entry
Database: PDB / ID: 1f78
TitleSOLUTION STRUCTURE OF RNASE P RNA (M1 RNA) P4 STEM OLIGORIBONUCLEOTIDE COMPLEXED WITH COBALT (III) HEXAMINE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsRNASE P RNA RIBOZYME, P4 DOMAIN
KeywordsRNA / RIBONUCLEASE P / RIBOZYME / TRANSFER RNA PROCESSING / P4 STEM / 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 26, 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,7942
Polymers8,6331
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 / -
Representativeminimized 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: enzymatically 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
Has protein modificationN

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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 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-PLOR3.84Brungerstructure solution
X-PLOR3.84Brungerrefinement
RefinementMethod: restrained molecular dynamics, simulated annealing / Software ordinal: 1
Details: The average structure is based on superposition of 11 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.7 Angstrom. A total ...Details: The average structure is based on superposition of 11 converged structures after refinement. The average RMS deviation between the ensemble and the average structure is 1.7 Angstrom. A total of 266 NOE-derived intramolecular distance constraints, 164 dihedral restraint and 48 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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