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- PDB-8i50: Crystal structure of DNA octamer containing GuNA[Me,Me] -

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Basic information

Entry
Database: PDB / ID: 8i50
TitleCrystal structure of DNA octamer containing GuNA[Me,Me]
ComponentsDNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')
KeywordsDNA / OLIGONUCLEOTIDE / MODIFIED BASE
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.95 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
DepositionJan 21, 2023Deposition 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*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,5891
Polymers2,5891
Non-polymers00
Water84747
1
A: DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')

A: DNA (5'-D(*GP*(OIQ)P*GP*(BRU)P*AP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1772
Polymers5,1772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area1920 Å2
ΔGint9 kcal/mol
Surface area2950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.266, 32.266, 80.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-142-

HOH

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Components

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


Mass: 2588.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
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 7.0, 0.012M Spermine tetrahydrochloride, 0.080M Potassium chloride, 0.020M Magnesium chloride hexahydrate
PH range: 7

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9199 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 0.95→40.34 Å / Num. obs: 16392 / % possible obs: 99.5 % / Redundancy: 18.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.014 / Χ2: 1.01 / Net I/σ(I): 34.6
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 1.6 / Num. measured obs: 5846 / Num. unique obs: 720 / CC1/2: 0.646 / Rpim(I) all: 0.458 / Rrim(I) all: 0.78 / Χ2: 0.95

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Processing

Software
NameVersionClassification
XDSVersion Mar 15,2919data reduction
Aimlessdata scaling
AutoSolphasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 0.95→26.4 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 1607 10.02 %
Rwork0.1682 --
obs0.1705 16039 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 168 0 47 215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006233
X-RAY DIFFRACTIONf_angle_d2.134359
X-RAY DIFFRACTIONf_dihedral_angle_d26.916104
X-RAY DIFFRACTIONf_chiral_restr0.06738
X-RAY DIFFRACTIONf_plane_restr0.01212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.980.28791270.28541129X-RAY DIFFRACTION87
0.98-1.020.22311360.20311225X-RAY DIFFRACTION94
1.02-1.060.18971440.19791267X-RAY DIFFRACTION97
1.06-1.110.16741410.14871286X-RAY DIFFRACTION98
1.11-1.160.13011420.12571308X-RAY DIFFRACTION99
1.16-1.240.16531470.13121328X-RAY DIFFRACTION100
1.24-1.330.1691480.14311313X-RAY DIFFRACTION100
1.33-1.470.17261490.14371352X-RAY DIFFRACTION100
1.47-1.680.15811490.13711341X-RAY DIFFRACTION100
1.68-2.110.16151560.15061386X-RAY DIFFRACTION100
2.11-100.23061680.19391497X-RAY DIFFRACTION100

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