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- PDB-3cqs: A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozym... -

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Basic information

Entry
Database: PDB / ID: 3cqs
TitleA 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases
Components
  • 13-mer substrate strand with 3'-OH, 2',5'-phosphodiester covalently linking 5th and 6th nucleotides
  • 19-mer ribozyme strand
  • 29-mer ribozyme strand with S9L synthetic linker at 13th position
KeywordsRNA / 2' / 5' phosphodiester / hairpin ribozyme / reaction-intermediate / transition-state stabilization / ribonuclease / phosphoryl-transfer
Function / homologyCOBALT HEXAMMINE(III) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsTorelli, A.T. / Spitale, R.C. / Krucinska, J. / Wedekind, J.E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme
Authors: Torelli, A.T. / Spitale, R.C. / Krucinska, J. / Wedekind, J.E.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 13-mer substrate strand with 3'-OH, 2',5'-phosphodiester covalently linking 5th and 6th nucleotides
B: 29-mer ribozyme strand with S9L synthetic linker at 13th position
C: 19-mer ribozyme strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9684
Polymers19,8073
Non-polymers1611
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-8.2 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.160, 93.160, 129.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain 13-mer substrate strand with 3'-OH, 2',5'-phosphodiester covalently linking 5th and 6th nucleotides


Mass: 4052.470 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Strand synthesized by Fidelity Systems, Inc (Gaithersburg, MD) using modified adenosine phosphoramidite to create 3'-OH, 2',5'-phosphodiester linkage between positions 5 and 6. Sequence ...Details: Strand synthesized by Fidelity Systems, Inc (Gaithersburg, MD) using modified adenosine phosphoramidite to create 3'-OH, 2',5'-phosphodiester linkage between positions 5 and 6. Sequence occurs naturally in tobacco ringspot virus satellite RNA.
#2: DNA/RNA hybrid 29-mer ribozyme strand with S9L synthetic linker at 13th position


Mass: 9762.989 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Strand synthesized by Dharmacon (Fayette, CO) and includes S9L linking residue in place of naturally-occurring adenosine 14. Sequence otherwise occurs naturally in tobacco ringspot virus satellite RNA.
#3: RNA chain 19-mer ribozyme strand


Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Strand synthesized by Dharmacon (Fayette, CO). Sequence occurs naturally in tobacco ringspot virus satellite RNA.
#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20.5% (w/v) PEG 2000 MME, 0.10 M Na cacodylate buffer, 0.25 M Li2SO4, 2.5 mM Co(NH3)6Cl3, 2 mM spermidine-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000 MME11
2Li2SO411
3spermidine11
4sodium cacodylate11
5Co(NH3)6Cl311
6PEG 2K MME12
7Li2SO412
8HEPES12
9spermidine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 7, 2007 / Details: confocal
RadiationMonochromator: Osmic confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→34.2 Å / Num. obs: 8458 / Observed criterion σ(I): -3 / Redundancy: 5.09 % / Biso Wilson estimate: 98.26 Å2 / Rsym value: 0.056 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 834 / Rsym value: 0.445

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2p7f

2p7f


Resolution: 2.8→22.92 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 889129.91 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: Parkinson et al. Acta Cryst. D, 52, 57-64 (1996)
Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 621 7.4 %Test set reflections matched to those of starting model. Additional reflections flagged at random to exclude 7.4% total.
Rwork0.217 ---
all0.22 8635 --
obs0.22 8446 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.8313 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 82.2 Å2
Baniso -1Baniso -2Baniso -3
1--13.93 Å20 Å20 Å2
2---13.93 Å20 Å2
3---27.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.91 Å0.96 Å
Refinement stepCycle: LAST / Resolution: 2.8→22.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1327 7 6 1340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d18
X-RAY DIFFRACTIONc_improper_angle_d1.83
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.524 101 7.4 %
Rwork0.521 1269 -
obs-1269 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rnaATTdna-rnaATT
X-RAY DIFFRACTION2cobalt.parcobalt.top
X-RAY DIFFRACTION3toto

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