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- PDB-1grz: A PREORGANIZED ACTIVE SITE IN THE CRYSTAL STRUCTURE OF THE TETRAH... -

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Basic information

Entry
Database: PDB / ID: 1grz
TitleA PREORGANIZED ACTIVE SITE IN THE CRYSTAL STRUCTURE OF THE TETRAHYMENA RIBOZYME
ComponentsLSU R-RNA GROUP I INTRON
KeywordsRIBOZYME / RIBOZYME STRUCTURE / RRNA GROUP I INTRON
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 5 Å
AuthorsGolden, B.L. / Gooding, A.R. / Podell, E.R. / Cech, T.R.
Citation
Journal: Science / Year: 1998
Title: A preorganized active site in the crystal structure of the Tetrahymena ribozyme.
Authors: Golden, B.L. / Gooding, A.R. / Podell, E.R. / Cech, T.R.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: A strategy for crystallization of a ribozyme derived from the Tetrahymena group I intron
Authors: Golden, B.L. / Podell, E.R. / Gooding, A.R. / Cech, T.R.
#2: Journal: Science / Year: 1996
Title: Crystal structure of a group I ribozyme domain: Principles of RNA packing
Authors: Cate, J.H. / Gooding, A.R. / Podell, E.R. / Zhou, K. / Golden, B.L. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
History
DepositionSep 14, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 24, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LSU R-RNA GROUP I INTRON
B: LSU R-RNA GROUP I INTRON


Theoretical massNumber of molelcules
Total (without water)159,7932
Polymers159,7932
Non-polymers00
Water00
1
A: LSU R-RNA GROUP I INTRON


Theoretical massNumber of molelcules
Total (without water)79,8961
Polymers79,8961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LSU R-RNA GROUP I INTRON


Theoretical massNumber of molelcules
Total (without water)79,8961
Polymers79,8961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.0, 179.0, 199.3
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number94
Cell settingtetragonal
Space group name H-MP42212

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Components

#1: RNA chain LSU R-RNA GROUP I INTRON


Mass: 79896.383 Da / Num. of mol.: 2 / Fragment: RESIDUES 332-402 DELETED, LOOP 6 REPLACED BY GAGA / Mutation: U322C, U323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 BLUE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.38 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlRNA1drop
210 mM1reservoirMgCl2
350 mMpotassium caodylate1reservoir
450 mM1reservoirKCl
50.5 mMspermine1reservoir
60.5 mMMPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 5→25 Å / Num. all: 14377 / Num. obs: 14377 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.052 / Net I/σ(I): 27
Reflection shellResolution: 5→5.18 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 10 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
PHASESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.4285 1139 9 %RANDOM
Rwork0.3686 ---
obs0.3686 11156 79.4 %-
Displacement parametersBiso mean: 169 Å2
Refinement stepCycle: LAST / Resolution: 5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 10578 0 0 10578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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