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- PDB-5k7e: The structure of pistol ribozyme, soaked with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5k7e
TitleThe structure of pistol ribozyme, soaked with Mn2+
Components
  • DNA/RNA 11-MER
  • RNA 47-MER
KeywordsRNA/DNA / ribozyme / RNA structure / pistol / RNA-DNA complex
Function / homology: / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 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 1.3Sep 27, 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 / 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)18,7214
Polymers18,6112
Non-polymers1102
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-18 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.986, 55.986, 89.460
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: containing 0.1 M Na-cacodylate, pH 6.5, 0.05 M Mg(OAc)2 and 32% MPD and supplemented with 150 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 3.27→89.5 Å / Num. obs: 3743 / % possible obs: 95.7 % / Redundancy: 3.1 % / Net I/σ(I): 9.4
Reflection shellResolution: 3.27→3.53 Å / % possible obs: 98.5 % / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.1 / Rpim(I) all: 0.589

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K7D

5k7d


Resolution: 3.27→48.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.29 194 -
Rwork0.24 --
obs-3743 95.7 %
Refinement stepCycle: LAST / Resolution: 3.27→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1237 2 2 1241

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