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- PDB-2oue: Crystal structure of a junctionless all-RNA hairpin ribozyme at 2... -

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Basic information

Entry
Database: PDB / ID: 2oue
TitleCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution
Components
  • Loop A ribozyme strand
  • Loop B S-turn strand
  • Loop B ribozyme strand
  • Substrate strand - Minimal Junctionless Hairpin Ribozyme
KeywordsRNA / hairpin ribozyme / all-RNA / mutation / low salt / S-turn / E-loop / ribose zipper / catalytic RNA
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsWedekind, J.E.
CitationJournal: Biochemistry / Year: 2006
Title: Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Authors: Salter, J. / Krucinska, J. / Alam, S. / Grum-Tokars, V. / Wedekind, J.E.
History
DepositionFeb 10, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionMar 6, 2007ID: 1ZFR
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 17, 2014Group: Non-polymer description
Revision 1.4Feb 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: Substrate strand - Minimal Junctionless Hairpin Ribozyme
B: Loop A ribozyme strand
C: Loop B ribozyme strand
D: Loop B S-turn strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9827
Polymers19,5644
Non-polymers4183
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.272, 93.272, 131.250
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 Substrate strand - Minimal Junctionless Hairpin Ribozyme


Mass: 4066.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized based on satellite tobacco ringspot virus
#2: RNA chain Loop A ribozyme strand


Mass: 3970.448 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized based on satellite tobacco ringspot virus
#3: RNA chain Loop B ribozyme strand


Mass: 5535.445 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized based on satellite tobacco ringspot virus
#4: RNA chain Loop B S-turn strand


Mass: 5991.568 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized based on satellite tobacco ringspot virus

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Non-polymers , 3 types, 87 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000 MME, LITHIUM SULFATE, cacodylate, spermidine, cobalt hexaamine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000 MME11
2LITHIUM SULFATE11
3cacodylate11
4spermidine11
5cobalt hexaamine11
6PEG 2000 MME12
7LITHIUM SULFATE12
8cacodylate12
9spermidine12
10cobalt hexaamine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2004
Details: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING
RadiationMonochromator: BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.05→30.4 Å / Num. obs: 21699 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 8.2 % / Biso Wilson estimate: 61.8 Å2 / Net I/σ(I): 24
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.432 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→30.4 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1422181.38 / Data cutoff high rms absF: 1422181.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1709 7.9 %RANDOM
Rwork0.252 ---
obs0.252 21645 99.1 %-
all-21669 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.093 Å2 / ksol: 0.343432 e/Å3
Displacement parametersBiso mean: 69.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.5 Å2-9.47 Å20 Å2
2---13.11 Å20 Å2
3---23.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.44 Å
Luzzati d res low-30 Å
Luzzati sigma a0.78 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.05→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1295 19 84 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d1.99
LS refinement shellResolution: 2.05→2.26 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.607 404 7.6 %
Rwork0.572 4892 -
obs--99.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ion.paramdna-rna.top
X-RAY DIFFRACTION2dna-rna_rep.paramcobalt.top
X-RAY DIFFRACTION3cobalt.parion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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