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- PDB-3i2q: Crystal structure of the hairpin ribozyme with 2'OMe substrate st... -

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Basic information

Entry
Database: PDB / ID: 3i2q
TitleCrystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9
Components
  • 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'
  • 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
  • DNA/RNA (30-MER)
KeywordsRNA / hairpin ribozyme / N1-deazaadenosine
Function / homologyCOBALT HEXAMMINE(III) / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å
AuthorsWedekind, J.E. / Spitale, R.C. / Krucinska, J.
CitationJournal: Biochemistry / Year: 2009
Title: Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.
Authors: Spitale, R.C. / Volpini, R. / Mungillo, M.V. / Krucinska, J. / Cristalli, G. / Wedekind, J.E.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / struct_conn / struct_ref_seq / 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_ref_seq.db_align_end / _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: 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'
B: DNA/RNA (30-MER)
C: 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)20,3835
Polymers20,1263
Non-polymers2572
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-3.6 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.350, 93.350, 131.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHE BIOLOGICAL UNIT IS THE SAME AS AN ASYMMETRIC UNIT

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Components

#1: RNA chain 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'


Mass: 4372.663 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The RNA was synthesized by Dharmacon Inc., following the tobacco ringspot virus sequence
#2: DNA/RNA hybrid DNA/RNA (30-MER)


Mass: 9762.001 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The RNA was synthesized by Dharmacon Inc., following the tobacco ringspot virus sequence
#3: RNA chain 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
Details: The RNA was synthesized by Dharmacon Inc., following the tobacco ringspot virus sequence
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6 / Details: Hairpin ribozyme

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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: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Well solutions contained 20.5% w/v PEG 2000 MME, 0.10 M Na cacodylate, pH 6.5 or 7.0, 0.25 M Li2SO4, 2.5 mM Co(NH3)6Cl3 and 2 mM Spermidine-HCl. Crystals grew as hexagonal rods or plates and ...Details: Well solutions contained 20.5% w/v PEG 2000 MME, 0.10 M Na cacodylate, pH 6.5 or 7.0, 0.25 M Li2SO4, 2.5 mM Co(NH3)6Cl3 and 2 mM Spermidine-HCl. Crystals grew as hexagonal rods or plates and reached a size of 0.3 mm x 0.2 mm x 0.2 mm in approximately 3 weeks, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Components of the solutions
IDNameCrystal-ID
1PEG 2000 MME1
2Na cacodylate1
3Li2SO41
4Co(NH3)6Cl31
5Spermidine-HCl1
6PEG 2000 MME1
7Na cacodylate1
8Li2SO41
9Co(NH3)6Cl31
10Spermidine-HCl1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2009
Details: Vertical focusing mirror, single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9310 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 132.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1645 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OUE

2oue


Resolution: 2.9→40.42 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 62866.93 / 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
Rfree0.227 607 7.6 %RANDOM
Rwork0.203 ---
obs0.203 7977 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.7653 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 73 Å2
Baniso -1Baniso -2Baniso -3
1--15.62 Å20 Å20 Å2
2---15.62 Å20 Å2
3---31.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.9→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1311 11 0 1322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_improper_angle_d2.41
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.448 113 8.8 %
Rwork0.424 1177 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rnaATTprotein.top
X-RAY DIFFRACTION2cobalt.par
X-RAY DIFFRACTION3to
X-RAY DIFFRACTION4to
X-RAY DIFFRACTION5to

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