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- PDB-5ckk: Crystal structure of 9DB1* deoxyribozyme -

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Basic information

Entry
Database: PDB / ID: 5ckk
TitleCrystal structure of 9DB1* deoxyribozyme
Components
  • DNA (44-MER)
  • RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)-3')
KeywordsLIGASE / deoxyribozyme / RNA-ligase / catalytic DNA
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsPonce-Salvatierra, A. / Hoebartner, C. / Pena, V.
CitationJournal: Nature / Year: 2016
Title: Crystal structure of a DNA catalyst.
Authors: Ponce-Salvatierra, A. / Wawrzyniak-Turek, K. / Steuerwald, U. / Hobartner, C. / Pena, V.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: DNA (44-MER)
D: RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5575
Polymers18,4842
Non-polymers733
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-29 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.155, 83.155, 55.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (44-MER)


Mass: 13651.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(P*GP*CP*AP*CP*UP*AP*GP*AP*UP*CP*GP*GP*AP*UP*G)-3')


Mass: 4831.938 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, spermine, magnesium chloride, sodium chloride, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→41.58 Å / Num. obs: 5146 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 25.8 % / Rmerge(I) obs: 6.13 / Mean I/σ(I) obs: 0.43 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CKI

5cki


Resolution: 2.801→46.446 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2872 249 4.98 %
Rwork0.2748 --
obs0.2755 4995 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→46.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1232 3 0 1235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151388
X-RAY DIFFRACTIONf_angle_d0.6592134
X-RAY DIFFRACTIONf_dihedral_angle_d30.205614
X-RAY DIFFRACTIONf_chiral_restr0.033251
X-RAY DIFFRACTIONf_plane_restr0.00459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-3.52870.40241170.27972234X-RAY DIFFRACTION94
3.5287-46.45260.27341320.27422512X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.3772 Å / Origin y: -23.6843 Å / Origin z: 9.4008 Å
111213212223313233
T1.3092 Å2-0.2404 Å2-0.1115 Å2-1.329 Å20.0195 Å2--0.5892 Å2
L5.9474 °20.2787 °2-3.4591 °2-3.3674 °21.7706 °2--5.8713 °2
S0.3726 Å °0.4383 Å °0.7633 Å °0.0438 Å °-0.1089 Å °0.2399 Å °-0.4431 Å °0.3141 Å °-0.285 Å °
Refinement TLS groupSelection details: chain 'D' or chain 'Y'

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