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- PDB-1ldz: SOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, 25 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1ldz
TitleSOLUTION STRUCTURE OF THE LEAD-DEPENDENT RIBOZYME, NMR, 25 STRUCTURES
ComponentsLEAD-DEPENDENT RIBOZYME
KeywordsRNA / CATALYTIC RNA / INTERNAL LOOPS / LEADZYME / NMR SPECTROSCOPY / RNA STRUCTURE
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING FROM RANDOM TORSION ANGLES
AuthorsHoogstraten, C.G. / Legault, P. / Pardi, A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: NMR solution structure of the lead-dependent ribozyme: evidence for dynamics in RNA catalysis.
Authors: Hoogstraten, C.G. / Legault, P. / Pardi, A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Order, Dynamics and Metal-Binding in the Lead-Dependent Ribozyme
Authors: Legault, P. / Hoogstraten, C.G. / Metlitzky, E. / Pardi, A.
#2: Journal: Biochemistry / Year: 1994
Title: Properties of an in Vitro Selected Pb2+ Cleavage Motif
Authors: Pan, T. / Dichtl, B. / Uhlenbeck, O.C.
#3: Journal: Nature / Year: 1992
Title: A Small Metalloribozyme with a Two-Step Mechanism
Authors: Pan, T. / Uhlenbeck, O.C.
#4: Journal: Biochemistry / Year: 1992
Title: In Vitro Selection of Rnas that Undergo Autolytic Cleavage with Pb2+
Authors: Pan, T. / Uhlenbeck, O.C.
History
DepositionAug 18, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEAD-DEPENDENT RIBOZYME


Theoretical massNumber of molelcules
Total (without water)9,7621
Polymers9,7621
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)25 / 25NO NOE VIOLATIONS GREATER THAN 0.3 A, NO DIHEDRAL VIOLATIONS GREATER THAN 3 DEGREES, GOOD STEREOCHEMICAL QUALITY, TOTAL ENERGY LESS THAN -120 KCAL/MOL, NOE PSEUDOENERGY LESS THAN 4 KCAL/ MOL
RepresentativeModel #1

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Components

#1: RNA chain LEAD-DEPENDENT RIBOZYME / LEADZYME


Mass: 9761.906 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PREPARED BY IN VITRO TRANSCRIPTION FROM SYNTHETIC DNA TEMPLATE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121CPMG-NOESY
131BD-NOESY
141CBD-NOESY
151NOESY-HSQC
161CBD-NOESY-HSQC
171HMQC-NOESY-HSQC
181(H)CCH-E.COSY
191DIRECTED HCC-TOCSY-CCH-E.COSY
1101SPIN-ECHO DIFFERENCE CT-(H)CCH-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED FROM DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED USING UNLABELED, 15N-LABELED, AND 13C, 15N-LABELED SAMPLES OF THE LEADZYME PREPARED BY IN VITRO TRANSCRIPTION.

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Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 0.1 M / pH: 5.5 / 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
Varian UNITYPLUSVarianUNITYPLUS5001
Bruker UNITYINOVABrukerUNITYINOVA6002
Bruker DMXBrukerDMX7503

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: SIMULATED ANNEALING FROM RANDOM TORSION ANGLES / Software ordinal: 1
Details: A COMPLETE SET OF REFINEMENT MACROS, ALONG WITH ASSOCIATED FILES, IS AVAILABLE UPON REQUEST TO THE AUTHORS.
NMR ensembleConformer selection criteria: NO NOE VIOLATIONS GREATER THAN 0.3 A, NO DIHEDRAL VIOLATIONS GREATER THAN 3 DEGREES, GOOD STEREOCHEMICAL QUALITY, TOTAL ENERGY LESS THAN -120 KCAL/MOL, NOE PSEUDOENERGY LESS THAN 4 KCAL/ MOL
Conformers calculated total number: 25 / Conformers submitted total number: 25

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