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- PDB-1c0o: SOLUTION STRUCTURE OF THE P5 HAIRPIN FROM A GROUP I INTRON COMPLE... -

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Entry
Database: PDB / ID: 1c0o
TitleSOLUTION STRUCTURE OF THE P5 HAIRPIN FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, 19 CONVERGED STRUCTURES
ComponentsRNA (5'-R(*GP*GP*GP*UP*CP*UP*UP*CP*GP*GP*GP*UP*CP*C)-3')
KeywordsRNA / RIBONUCLEIC ACID / COBALT (III) HEXAMMINE / METAL BINDING / RNA STRUCTURE
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsColmenarejo, G. / Tinoco Jr., I.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme.
Authors: Colmenarejo, G. / Tinoco Jr., I.
History
DepositionMar 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: 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 (5'-R(*GP*GP*GP*UP*CP*UP*UP*CP*GP*GP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6332
Polymers4,4721
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)19 / 40NOE ENERGY (LEAST RESTRAINT VIOLATIONS), DIHEDRAL ENERGY (LEAST RESTRAINT VIOLATIONS), TOTAL ENERGY
Representative

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Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*UP*CP*UP*UP*CP*GP*GP*GP*UP*CP*C)-3')


Mass: 4471.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLOSED BY A UUCG TETRALOOP; COBALT (III) HEXAMMINE BINDS AT THE MAJOR GROOVE OF TWO TANDEM G-U WOBBLE PAIRS IN 5'-GU-3' ORIENTATION
Source: (gene. exp.) Tetrahymena thermophila (eukaryote)
Description: SYNTHESIZED ENZYMATICALLY IN-VITRO USING 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
111DQF-COSY
121D2O NOESY
131H2O NOESY
141TOCSY
15113C-1H HMQC
16131P-1H HETCOR
17131P-1H TOCSY
18131P-1H TOCSY-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. ALL 13C EXPERIMENTS WERE DONE USING NATURAL ABUNDANCE. COBALT (III) HEXAMMINE WAS LOCATED USING DOCKING WITH 7 ...Text: THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. ALL 13C EXPERIMENTS WERE DONE USING NATURAL ABUNDANCE. COBALT (III) HEXAMMINE WAS LOCATED USING DOCKING WITH 7 INTERMOLECULAR NOES OBSERVED IN 2D WATER NOESY EXPERIMENTS.

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Sample preparation

DetailsContents: PHOSPHATE BUFFER, EDTA
Sample conditionsIonic strength: 100 mM NACL / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6005001
Bruker DRX500BrukerDRX5006002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
FELIX95structure solution
X-PLOR3.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NOE ENERGY (LEAST RESTRAINT VIOLATIONS), DIHEDRAL ENERGY (LEAST RESTRAINT VIOLATIONS), TOTAL ENERGY
Conformers calculated total number: 40 / Conformers submitted total number: 19

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