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- PDB-1x8w: Structure of the Tetrahymena Ribozyme: Base Triple Sandwich and M... -

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Basic information

Entry
Database: PDB / ID: 1x8w
TitleStructure of the Tetrahymena Ribozyme: Base Triple Sandwich and Metal Ion at the Active Site
ComponentsTetrahymena ribozyme RNA
KeywordsRNA / Catalytic RNA / ribozyme / group I intron / guanosine binding site / metal ions / active site / catalytic mechanism / base triples / conformational changes
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.8 Å
AuthorsGuo, F. / Gooding, A.R. / Cech, T.R.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site.
Authors: Guo, F. / Gooding, A.R. / Cech, T.R.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrahymena ribozyme RNA
B: Tetrahymena ribozyme RNA
C: Tetrahymena ribozyme RNA
D: Tetrahymena ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,78942
Polymers319,8664
Non-polymers92438
Water00
1
A: Tetrahymena ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,20911
Polymers79,9661
Non-polymers24310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetrahymena ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18510
Polymers79,9661
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tetrahymena ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18510
Polymers79,9661
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tetrahymena ribozyme RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,20911
Polymers79,9661
Non-polymers24310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.400, 175.400, 304.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain
Tetrahymena ribozyme RNA


Mass: 79966.438 Da / Num. of mol.: 4 / Mutation: A210G, U259A, A269G, U277C, A304G / Source method: obtained synthetically
Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION. The sequence of this RNA can be found naturally in TETRAHYMENA THERMOPHILA.
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 9.5% 2-methyl-2,4-pentanediol (MPD), 25 mM K cacodylate pH 6.0, 25 mM KCl, 5mM NaCl, 17.5 mM MgCl2 and 0.25 mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2cacodylate11
3KCl11
4NaCl11
5MgCl211
6spermine11
7H2O11
8cacodylate12
9KCl12
10NaCl12
11MgCl212
12H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2002 / Details: Double crystal, Si(111)
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.8→20 Å / Num. all: 43985 / Num. obs: 43972 / % possible obs: 93.9 % / Observed criterion σ(F): 0.01 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 24
Reflection shellResolution: 3.8→3.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4429 / % possible all: 76.8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 3.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: experimental phase probability distribution is used in the maximum likehood target
RfactorNum. reflectionSelection details
Rfree0.32 3102 Random
Rwork0.263 --
all0.267 43985 -
obs0.267 43972 -
Displacement parametersBiso mean: 122 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.81 Å0.63 Å
Luzzati d res low-20 Å
Luzzati sigma a0.67 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 20754 38 0 20792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.5
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.59
LS refinement shellResolution: 3.8→3.97 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.391 315 -
Rwork0.345 --
obs--72.8 %

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