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- PDB-6lbw: Crystal structure of Ag-mediated base pairs in uncanonical DNA duplex -

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Basic information

Entry
Database: PDB / ID: 6lbw
TitleCrystal structure of Ag-mediated base pairs in uncanonical DNA duplex
ComponentsDNA (5'-D(*CP*GP*(CBR)P*GP*AP*(LCC)P*TP*CP*GP*CP*G)-3')
KeywordsDNA / LNA / 2' / 4'-BNA / metallo-base pair / silver
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.501 Å
AuthorsAoyama, H. / Obika, S. / Nakagawa, O.
CitationJournal: Chemistry / Year: 2021
Title: Crystallographic Structure of Novel Types of Ag I -Mediated Base Pairs in Non-canonical DNA Duplex Containing 2'-O,4'-C-Methylene Bridged Nucleic Acids.
Authors: Nakagawa, O. / Aoyama, H. / Fujii, A. / Kishimoto, Y. / Obika, S.
History
DepositionNov 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,1284
Polymers6,9122
Non-polymers2162
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-7 kcal/mol
Surface area3370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.560, 68.110, 118.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

21B-125-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*GP*(CBR)P*GP*AP*(LCC)P*TP*CP*GP*CP*G)-3')


Mass: 3456.107 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9195 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.5→34.055 Å / Num. obs: 17630 / % possible obs: 98.3 % / Redundancy: 3.314 % / Biso Wilson estimate: 29.464 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.099 / Χ2: 1.561 / Net I/σ(I): 8.16 / Num. measured all: 58431
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.593.1580.9461.218941289828310.3921.14497.7
1.59-1.73.3990.6252.259093272226750.7580.74498.3
1.7-1.843.3160.3114.28177252024660.9280.37297.9
1.84-2.013.2040.1956.177271234122690.9660.23596.9
2.01-2.253.2310.1668.96744210420870.9640.299.2
2.25-2.63.6360.10214.16766186918610.9820.12199.6
2.6-3.173.4620.07217.425445158915730.9890.08699
3.17-4.473.0710.05919.513615120311770.990.07197.8
4.47-34.0553.4430.05221.523796986910.9940.06199

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.501→34.055 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 32.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 1740 9.88 %
Rwork0.2143 15876 -
obs0.2172 17616 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.27 Å2 / Biso mean: 27.1068 Å2 / Biso min: 15.07 Å2
Refinement stepCycle: final / Resolution: 1.501→34.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 450 2 58 510
Biso mean--21.9 35.96 -
Num. residues----22
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.501-1.54480.50861380.4271131197
1.5448-1.59470.37411420.4141132897
1.5947-1.65170.42261440.3548130298
1.6517-1.71780.33871490.3306133098
1.7178-1.7960.31450.2892132398
1.796-1.89070.31041410.3059131597
1.8907-2.00910.3261470.2797128097
2.0091-2.16420.28441460.2385132899
2.1642-2.38190.20671500.1911364100
2.3819-2.72650.23021450.1805131699
2.7265-3.43460.19651460.1831135298
3.4346-100.19681470.1652132798
Refinement TLS params.Method: refined / Origin x: 10.3234 Å / Origin y: 25.4265 Å / Origin z: 14.5736 Å
111213212223313233
T0.1868 Å2-0.0147 Å2-0.0122 Å2-0.19 Å20.0198 Å2--0.1843 Å2
L0.0243 °2-0.0331 °20.0425 °2-0.0536 °2-0.0589 °2--0.0737 °2
S-0.0624 Å °-0.0653 Å °0.0913 Å °-0.0993 Å °-0.0824 Å °-0.168 Å °0.0389 Å °-0.0942 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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