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- PDB-9kl1: Crystal structure of DNA/RNA duplex obtained using the counter di... -

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Basic information

Entry
Database: PDB / ID: 9kl1
TitleCrystal structure of DNA/RNA duplex obtained using the counter diffusion method in space (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: 1.6 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

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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
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint1 kcal/mol
Surface area3490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.015, 49.015, 45.706
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.: 49 / 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: 2.81 Å3/Da / Density % sol: 56.21 %
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: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→31.1 Å / Num. obs: 8323 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.027 / Rrim(I) all: 0.03 / Net I/σ(I): 26.02
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.70.32813530.9490.3651
1.7-1.80.18610840.9770.2081
1.8-1.90.1378700.9880.1521
1.9-20.0956900.9930.1061
2-30.0429970.9990.0451
3-40.0273810.0221
4-50.01926810.0211
5-31.10.0192840.9990.0211

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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: 1.6→31.1 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 835 10.03 %
Rwork0.1958 --
obs0.1972 8323 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 14 49 437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.032
X-RAY DIFFRACTIONf_angle_d1.228
X-RAY DIFFRACTIONf_dihedral_angle_d13.111189
X-RAY DIFFRACTIONf_chiral_restr0.07178
X-RAY DIFFRACTIONf_plane_restr0.00718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70.25631310.24321236X-RAY DIFFRACTION99
1.7-1.830.2311380.19511235X-RAY DIFFRACTION100
1.83-2.010.24091420.24041239X-RAY DIFFRACTION100
2.01-2.30.25591360.25111264X-RAY DIFFRACTION100
2.3-2.90.26931460.25111246X-RAY DIFFRACTION100
2.9-31.10.16911420.15461268X-RAY DIFFRACTION100

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