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- PDB-8his: Crystal structure of DNA decamer containing GuNA[Me,tBu] -

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Basic information

Entry
Database: PDB / ID: 8his
TitleCrystal structure of DNA decamer containing GuNA[Me,tBu]
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3')
KeywordsDNA / OLIGONUCLEOTIDE / MODIFIED BASE
Function / homologyCACODYLIC ACID / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsAoyama, H. / Obika, S. / Yamaguchi, T.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05748 Japan
Japan Society for the Promotion of Science (JSPS)21K06511 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101084 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0301004 Japan
Japan Agency for Medical Research and Development (AMED)19am0401003 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121022 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae0121023 Japan
Japan Agency for Medical Research and Development (AMED)JP21ae012102 Japan
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids.
Authors: Yamaguchi, T. / Horie, N. / Aoyama, H. / Kumagai, S. / Obika, S.
History
DepositionNov 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5063
Polymers6,3682
Non-polymers1381
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint1 kcal/mol
Surface area3880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.070, 44.360, 45.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*(LR6)P*AP*CP*GP*C)-3')


Mass: 3184.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040M Sodium cacodylate trihydrate pH 6.0, 0.012M Spermine tetrahydrochloride, 0.080M Potassium chloride, 0.020M Barium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→20.13 Å / Num. obs: 6474 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Χ2: 0.94 / Net I/σ(I): 55.1
Reflection shellResolution: 2.01→2.07 Å / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Num. measured all: 1890 / Num. unique obs: 294 / CC1/2: 0.998 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Χ2: 0.83 / Net I/σ(I) obs: 43.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å20.13 Å
Translation2.01 Å20.13 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I5W

1i5w


Resolution: 2.01→20.13 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 664 10.26 %
Rwork0.1778 --
obs0.1831 6474 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→20.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 424 5 91 520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005478
X-RAY DIFFRACTIONf_angle_d1.911740
X-RAY DIFFRACTIONf_dihedral_angle_d18.172208
X-RAY DIFFRACTIONf_chiral_restr0.07281
X-RAY DIFFRACTIONf_plane_restr0.00424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.160.2571240.19991157X-RAY DIFFRACTION99
2.16-2.380.26161290.20411167X-RAY DIFFRACTION99
2.38-2.720.25031400.21671171X-RAY DIFFRACTION100
2.73-3.430.24831360.17931149X-RAY DIFFRACTION100
3.43-20.130.17621350.141166X-RAY DIFFRACTION100

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