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- PDB-7sdg: [C:Ag+:C] Metal-mediated DNA base pair in a self-assembling rhomb... -

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Basic information

Entry
Database: PDB / ID: 7sdg
Title[C:Ag+:C] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.63 Å
AuthorsVecchioni, S. / Lu, B. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, 6items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)2106790 United States
Human Frontier Science Program (HFSP)RPG0010/2017 United States
National Science Foundation (NSF, United States)DMR-1420073 United States
National Aeronautic Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
CitationJournal: Adv Mater / Year: 2023
Title: Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction.
Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. ...Authors: Vecchioni, S. / Lu, B. / Livernois, W. / Ohayon, Y.P. / Yoder, J.B. / Yang, C.F. / Woloszyn, K. / Bernfeld, W. / Anantram, M.P. / Canary, J.W. / Hendrickson, W.A. / Rothschild, L.J. / Mao, C. / Wind, S.J. / Seeman, N.C. / Sha, R.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9736
Polymers12,7574
Non-polymers2162
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,91918
Polymers38,27212
Non-polymers6476
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)105.984, 105.984, 90.264
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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


Mass: 6448.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')


Mass: 2051.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
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: 8.41 Å3/Da / Description: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: MOPS, Magnesium sulfate, Silver nitrate / Temp details: 338-293 at 0.4/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 3.627→64.357 Å / Num. obs: 2608 / % possible obs: 84.7 % / Redundancy: 10.8 % / Biso Wilson estimate: 281.2 Å2 / CC1/2: 1 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
3.627-4.05610.20.61990.082144
10.066-64.35711.627.420011100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.63→32.38 Å / SU ML: 0.2004 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 44.7372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 254 4.88 %
Rwork0.1875 4950 -
obs0.1888 2602 60.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 291.33 Å2
Refinement stepCycle: LAST / Resolution: 3.63→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 2 0 858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117956
X-RAY DIFFRACTIONf_angle_d1.23161467
X-RAY DIFFRACTIONf_chiral_restr0.0649167
X-RAY DIFFRACTIONf_plane_restr0.007542
X-RAY DIFFRACTIONf_dihedral_angle_d39.2534407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.63-4.570.4041700.4064619X-RAY DIFFRACTION30.43
4.57-32.380.20041840.17863712X-RAY DIFFRACTION91.28

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