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- PDB-5k7c: The native structure of native pistol ribozyme -

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Basic information

Entry
Database: PDB / ID: 5k7c
TitleThe native structure of native pistol ribozyme
Components
  • DNA/RNA 11-MER
  • RNA 47-MER
KeywordsRNA/DNA / ribozyme / RNA structure / pistol / RNA-DNA complex
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsRen, A. / Patel, D.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.
Authors: Ren, A. / Vusurovic, N. / Gebetsberger, J. / Gao, P. / Juen, M. / Kreutz, C. / Micura, R. / Patel, D.J.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA 47-MER
B: DNA/RNA 11-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6845
Polymers18,6112
Non-polymers733
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-29 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.196, 56.196, 89.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA/RNA hybrid RNA 47-MER


Mass: 15096.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA/RNA hybrid DNA/RNA 11-MER


Mass: 3514.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na-cacodylate, pH 6.5, Mg(OAc)2 0.2 M and 32% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.73→89.3 Å / Num. obs: 4612 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rpim(I) all: 0.037 / Net I/σ(I): 12.8
Reflection shellResolution: 2.73→2.86 Å / % possible obs: 100 % / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.9 / Rpim(I) all: 0.727

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→48.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 228 -
Rwork0.2 --
obs-4612 99.8 %
Refinement stepCycle: LAST / Resolution: 2.73→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1237 3 1 1241

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