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- PDB-9kkz: Crystal structure of DNA/RNA duplex obtained using the counter di... -

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Basic information

Entry
Database: PDB / ID: 9kkz
TitleCrystal structure of DNA/RNA duplex obtained using the counter diffusion method on Earth (Na form)
Components
  • DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
KeywordsDNA/RNA / counter diffusion method / DNA-RNA complex
Function / homologySPERMINE / DNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKondo, J. / Ando, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121014 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: The first report of structural analysis of a nucleic acid using crystals grown in space.
Authors: Ando, S. / Takahashi, M. / Kondo, J.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
B: DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8453
Polymers5,6432
Non-polymers2021
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint1 kcal/mol
Surface area3490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.843, 48.843, 45.761
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Mass: 2981.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*(5CM)P*TP*CP*TP*TP*CP*TP*TP*(5CM))-3')


Mass: 2660.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 293.15 K / Method: counter-diffusion / Details: sodium chloride, MPD, spermine 4HCl, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→31.1 Å / Num. obs: 10053 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.029 / Net I/σ(I): 27.78
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.5-1.60.2317660.9710.2561
1.6-1.70.1113560.9940.1231
1.7-1.80.07310920.9960.0811
1.8-1.90.0588490.9970.0651
1.9-20.0477020.9970.0521
2-30.0329760.9990.0341
3-40.0247310.9990.0261
4-50.0232580.9990.0261
5-31.10.0212820.9990.0241

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.06 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1020 10.15 %
Rwork0.1927 --
obs0.1946 10053 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 14 62 450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.056
X-RAY DIFFRACTIONf_dihedral_angle_d11.223189
X-RAY DIFFRACTIONf_chiral_restr0.04178
X-RAY DIFFRACTIONf_plane_restr0.00718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.580.2581480.24891303X-RAY DIFFRACTION100
1.58-1.680.28421390.22281276X-RAY DIFFRACTION100
1.68-1.810.24891490.21531291X-RAY DIFFRACTION100
1.81-1.990.27271420.2231270X-RAY DIFFRACTION100
1.99-2.270.25531470.24581286X-RAY DIFFRACTION100
2.27-2.860.24631440.22751297X-RAY DIFFRACTION100
2.87-31.060.17011510.1561310X-RAY DIFFRACTION99

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