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- PDB-1x9k: An all-RNA Hairpin Ribozyme with mutation U39C -

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Basic information

Entry
Database: PDB / ID: 1x9k
TitleAn all-RNA Hairpin Ribozyme with mutation U39C
Components
  • 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3'
  • 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'
  • 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'
  • 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3'
KeywordsRNA / Hairpin ribozyme / all-RNA / mutation / high salt / S-turn / E-loop / catalytic RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsAlam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E.
Citation
Journal: Biochemistry / Year: 2005
Title: Conformational Heterogeneity at Position U37 of an All-RNA Hairpin Ribozyme with Implications for Metal Binding and the Catalytic Structure of the S-Turn.
Authors: Alam, S. / Grum-Tokars, V. / Krucinska, J. / Kundracik, M.L. / Wedekind, J.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme
Authors: Grum-Tokars, V. / Milovanovic, M. / Wedekind, J.E.
History
DepositionAug 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,8344
Polymers19,8344
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.46, 94.46, 129.12
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 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3'


Mass: 4055.421 Da / Num. of mol.: 1 / Mutation: U39C / Source method: obtained synthetically / Details: Solid Phase Chemical Synthesis
#2: RNA chain 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3'


Mass: 4251.654 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain 5'-R(*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 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, spermidine, cobalt hexaamine, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2spermidine11
3cobalt hexaamine11
4cacodylate11
5H2O11
6ammonium sulfate12
7cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 17, 2002
Details: insertion device, double crystal monochromator, vertical focusing mirror
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.17→25 Å / Num. obs: 6480 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 71.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 13.4
Reflection shellResolution: 3.17→3.28 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 594 / Rsym value: 0.412 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M5K

1m5k


Resolution: 3.17→24.63 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 13729086.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3
Stereochemistry target values: Parkinson et al., (1996) Acta Cryst. D52, 57-64
RfactorNum. reflection% reflectionSelection details
Rfree0.252 648 10.5 %RANDOM
Rwork0.236 ---
all0.243 6192 --
obs0.236 6161 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.1897 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 160.9 Å2
Baniso -1Baniso -2Baniso -3
1--21.28 Å2-34.31 Å20 Å2
2--13.14 Å20 Å2
3---8.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.71 Å0.72 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å1.03 Å
Refinement stepCycle: LAST / Resolution: 3.17→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1313 0 0 1313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.17→3.49 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.457 147 9.8 %
Rwork0.517 1346 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: DNA-RNA_REP.PARAM / Topol file: DNA-RNA.TOP

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