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- PDB-9k8o: Crystal structure of a short zinc-dependent DNAzyme minGAA -

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Basic information

Entry
Database: PDB / ID: 9k8o
TitleCrystal structure of a short zinc-dependent DNAzyme minGAA
Components
  • DNAzyme minGAA, catalytic strand
  • substrate strand for DNAzyme minGAA
KeywordsDNA-RNA HYBRID / DNAzyme / RNA cleavage / Zinc-dependent
Function / homologyDNA / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsYamasaki, K. / Yamasaki, T. / Kubota, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A minimal Zn2+-dependent RNA-cleaving DNAzyme and its B-DNA-like crystal and solution structures
Authors: Yamasaki, K. / Inomata, R. / Yamasaki, T. / Kubota, T. / Miyashita, N. / Takeuchi, K. / Miyagishi, M.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNAzyme minGAA, catalytic strand
B: substrate strand for DNAzyme minGAA
C: DNAzyme minGAA, catalytic strand
D: substrate strand for DNAzyme minGAA
E: DNAzyme minGAA, catalytic strand
F: substrate strand for DNAzyme minGAA
G: DNAzyme minGAA, catalytic strand
H: substrate strand for DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,09711
Polymers25,9018
Non-polymers1963
Water41423
1
A: DNAzyme minGAA, catalytic strand
B: substrate strand for DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5413
Polymers6,4752
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-24 kcal/mol
Surface area3670 Å2
MethodPISA
2
C: DNAzyme minGAA, catalytic strand
D: substrate strand for DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5413
Polymers6,4752
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-31 kcal/mol
Surface area3460 Å2
MethodPISA
3
E: DNAzyme minGAA, catalytic strand
F: substrate strand for DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5413
Polymers6,4752
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-22 kcal/mol
Surface area3680 Å2
MethodPISA
4
G: DNAzyme minGAA, catalytic strand
H: substrate strand for DNAzyme minGAA


Theoretical massNumber of molelcules
Total (without water)6,4752
Polymers6,4752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-2 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.861, 81.881, 81.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: DNA chain
DNAzyme minGAA, catalytic strand


Mass: 2989.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA/RNA hybrid
substrate strand for DNAzyme minGAA


Mass: 3485.272 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% MPD, 40 mM sodium cacodylate (7.0), 12 mM spermine, 80 mM NaCl, 12 mM KCl, 1 mM ZnCl2, and 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.04→40.94 Å / Num. obs: 5372 / % possible obs: 99.4 % / Redundancy: 6.29 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.9
Reflection shellResolution: 3.04→3.22 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1525 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.04→40.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.902 / SU B: 28.366 / SU ML: 0.509 / Cross valid method: THROUGHOUT / ESU R Free: 0.529 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29728 267 5 %RANDOM
Rwork0.20544 ---
obs0.20995 5105 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.974 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 3.04→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1658 3 23 1684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0111855
X-RAY DIFFRACTIONr_bond_other_d0.0030.02907
X-RAY DIFFRACTIONr_angle_refined_deg1.331.1782846
X-RAY DIFFRACTIONr_angle_other_deg1.5492.9732143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02990
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02448
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.6910.4031855
X-RAY DIFFRACTIONr_scbond_other9.68910.4041854
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.49715.5962846
X-RAY DIFFRACTIONr_long_range_B_refined19.65695.5652717
X-RAY DIFFRACTIONr_long_range_B_other19.65895.5432717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.04→3.116 Å
RfactorNum. reflection% reflection
Rfree0.432 17 -
Rwork0.382 336 -
obs--93.39 %

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