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- PDB-2cd6: Refinement of RNase P P4 stemloop structure using residual dipola... -

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Basic information

Entry
Database: PDB / ID: 2cd6
TitleRefinement of RNase P P4 stemloop structure using residual dipolar coupling data, C70U mutant cobalt(III) hexammine complex
Components5'-R(*GP*GP*AP*AP*GP*UP*UP*CP*CP*GP *UP*CP*UP*UP*CP*GP*GP*AP*CP*CP*GP*GP*CP*UP*UP*CP*C)-3'
KeywordsNUCLEIC ACID / C70U MUTANT / COBALT (III HEXAMMINE COMPLEX / METAL BINDING SITE / METAL COMPLEX / P4 STEM / RIBONUCLEASE P / RIBONUCLEIC ACID / RIBOZYME / TRANSFER RNA PROCESSING
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
Model type detailsMINIMIZED AVERAGE
AuthorsSchmitz, M.
History
DepositionJan 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Derived calculations / Other / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*AP*AP*GP*UP*UP*CP*CP*GP *UP*CP*UP*UP*CP*GP*GP*AP*CP*CP*GP*GP*CP*UP*UP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7952
Polymers8,6341
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 / 50LEAST RESTRAINT VIOLATION
Representative

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Components

#1: RNA chain 5'-R(*GP*GP*AP*AP*GP*UP*UP*CP*CP*GP *UP*CP*UP*UP*CP*GP*GP*AP*CP*CP*GP*GP*CP*UP*UP*CP*C)-3' / RNASE P RIBOZYME / P4 DOMAIN MUTANT


Mass: 8634.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTATION CYTOSINE 70 URACIL / Source: (synth.) ESCHERICHIA COLI (E. coli)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
Sequence detailsTHE SEQUENCE CORRESPONDS TO NUCLEOTIDES 66 TO 73, AND 354 TO 360 OF THE E. COLI RNASE P RNA, WITH ...THE SEQUENCE CORRESPONDS TO NUCLEOTIDES 66 TO 73, AND 354 TO 360 OF THE E. COLI RNASE P RNA, WITH TWO G:C PAIRS ADDED ON THE 5' SIDE OF THE HELIX, AND ONE U:A PAIR, ONE C:G PAIR AND A UUCG LOOP ADDED ON THE OTHER SIDE. IN THE PDB ENTRY,NUCLEOTIDES 3-10 CORRESPOND TO 66-73 IN E. COLI RNASE P RNA, AND NUCLEOTIDES 19-25 CORRESPOND TO 334-360.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 1H-15N HSCQ
NMR detailsText: THE STRUCTURE WAS DETERMINED USING CONSTRAINTS FROM HOMONUCLEAR NMR EXPERIMENTS AS DESCRIBED IN ENTRY 17F9, AND ADDITIONAL RESIDUAL DIPOLAR COUPLINGS FOR IMINO RESONANCES AQCUIRED WITH AND ...Text: THE STRUCTURE WAS DETERMINED USING CONSTRAINTS FROM HOMONUCLEAR NMR EXPERIMENTS AS DESCRIBED IN ENTRY 17F9, AND ADDITIONAL RESIDUAL DIPOLAR COUPLINGS FOR IMINO RESONANCES AQCUIRED WITH AND WITHOUT 30 MG PER ML PF1 PHAGE PRESENT IN SOLUTION

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 288.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIHNIHBRUNGERrefinement
Xplor-NIHNIHstructure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: DETAILS OF THE REFINEMENT PROCEDURE AGAINST RESIDUAL DIPOLAR COUPLINGS ARE GIVEN IN THE PRIMARY CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 1

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