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- PDB-3gs8: An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-s... -

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Basic information

Entry
Database: PDB / ID: 3gs8
TitleAn all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand
Components
  • RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3')
  • RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3')
  • RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')
  • RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')
KeywordsRNA / hairpin ribozyme / RNA ribozyme / N1-deazaadenosine
Function / homologyCOBALT HEXAMMINE(III) / Chem-S9L / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsSpitale, R.C. / Volpini, R. / Heller, M.G. / Krucinska, J. / Cristalli, G. / Wedekind, J.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Identification of an imino group indispensable for cleavage by a small ribozyme.
Authors: Spitale, R.C. / Volpini, R. / Heller, M.G. / Krucinska, J. / Cristalli, G. / Wedekind, J.E.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3')
B: RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3')
C: RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')
D: RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5058
Polymers19,8564
Non-polymers6484
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.820, 93.820, 134.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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RNA chain , 4 types, 4 molecules ABCD

#1: RNA chain RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3')


Mass: 4358.636 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3')


Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3')


Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: RNA chain RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3')


Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-S9L / 2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN PHOSPHATE


Mass: 230.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O7P
#7: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6

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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: 4.31 Å3/Da / Density % sol: 71.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20.5% (w/v) PEG 2K MME, 0.10 M Na-Cacodylate, 0.25 M Li2SO4, 2.5 mM Co(NH3)6Cl3, 2 mM spermidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2K MME11
2Na-Cacodylate11
3Li2SO411
4Co(NH3)6Cl311
5spermidine-HCl11
6PEG 2K MME12
7Na-Cacodylate12
8Li2SO412
9Co(NH3)6Cl312
10spermidine-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 8, 2008 / Details: VariMax optics (Rigaku)
RadiationMonochromator: 0.3 x 3 mm focusing cup operated at 4.8 kW / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.85→38.5 Å / Num. obs: 8407 / Observed criterion σ(I): 12.2 / Redundancy: 3.81 % / Biso Wilson estimate: 1.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.2 / Num. unique all: 830

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.85→27.37 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 79272.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 649 7.7 %RANDOM
Rwork0.22 ---
obs0.22 8402 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.382 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 96.9 Å2
Baniso -1Baniso -2Baniso -3
1--15.21 Å20 Å20 Å2
2---15.21 Å20 Å2
3---30.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a1.12 Å1.17 Å
Refinement stepCycle: LAST / Resolution: 2.85→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1313 32 0 1345
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d16.7
X-RAY DIFFRACTIONc_improper_angle_d2.25
LS refinement shellResolution: 2.85→2.95 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.548 110 7.9 %
Rwork0.525 1284 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rnaATTprotein.top
X-RAY DIFFRACTION2cobalt.par

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