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- PDB-9k8z: Crystal structure of DNA/RNA duplex obtained using the counter di... -

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Basic information

Entry
Database: PDB / ID: 9k8z
TitleCrystal structure of DNA/RNA duplex obtained using the counter diffusion method in space (K 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')
KeywordsRNA/DNA / counter diffusion method / space / microgravity / RNA-DNA complex
Function / homologySPERMINE / DNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
DepositionOct 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 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
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-2 kcal/mol
Surface area3490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.656, 48.656, 45.738
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.: 74 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293.15 K / Method: counter-diffusion / Details: potassium chloride, MPD, spermine, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→24.33 Å / Num. obs: 12207 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.042 / Net I/σ(I): 20.74
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.43-1.440.3512220.930.3861
1.44-1.450.3892460.9150.4291
1.45-1.460.3622070.910.3991
1.46-1.470.3862310.9040.4261
1.47-1.50.276140.9460.2971
1.5-1.60.19917170.9760.221
1.6-20.07839910.9960.0871
2-30.04329440.9990.0481
3-40.0327330.9990.0351
4-50.032530.9980.0331
5-24.330.0252850.9990.0281

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U6M

4u6m


Resolution: 1.4→24.33 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 1236 10.13 %
Rwork0.1851 --
obs0.1862 12207 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 14 74 462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.037
X-RAY DIFFRACTIONf_dihedral_angle_d10.619189
X-RAY DIFFRACTIONf_chiral_restr0.03878
X-RAY DIFFRACTIONf_plane_restr0.00818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.25871400.2621192X-RAY DIFFRACTION98
1.45-1.520.26221400.231225X-RAY DIFFRACTION100
1.52-1.60.24741320.21841188X-RAY DIFFRACTION100
1.6-1.70.22841370.21881222X-RAY DIFFRACTION100
1.7-1.830.22551390.20451222X-RAY DIFFRACTION100
1.83-2.020.24411390.20771216X-RAY DIFFRACTION100
2.02-2.310.21011400.20971227X-RAY DIFFRACTION100
2.31-2.910.20771320.20931234X-RAY DIFFRACTION100
2.91-24.330.15381370.14551245X-RAY DIFFRACTION100

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