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- PDB-8dx1: [C:Hg2+/Ag+:C--pH 7 MOPS] Metal-mediated DNA base pair in tensegr... -

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Basic information

Entry
Database: PDB / ID: 8dx1
Title[C:Hg2+/Ag+:C--pH 7 MOPS] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution in MOPS
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: 4.79 Å
AuthorsLu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 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 France
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: J.Am.Chem.Soc. / Year: 2023
Title: Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals.
Authors: Lu, B. / Ohayon, Y.P. / Woloszyn, K. / Yang, C.F. / Yoder, J.B. / Rothschild, L.J. / Wind, S.J. / Hendrickson, W.A. / Mao, C. / Seeman, N.C. / Canary, J.W. / Sha, R. / Vecchioni, S.
History
DepositionAug 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 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_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)13,0666
Polymers12,7574
Non-polymers3082
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)39,19818
Polymers38,27212
Non-polymers9256
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)106.180, 106.180, 88.077
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

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DNA chain , 4 types, 4 molecules ABCD

#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)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION

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Details

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: 7.49 Å3/Da / Density % sol: 83.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mM MOPS, 125 mM magnesium sulfate, 12 uM silver nitrate, 24 uM mercury chloride
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, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 4.79→53.09 Å / Num. obs: 2404 / % possible obs: 84.1 % / Redundancy: 10.4 % / Biso Wilson estimate: 247.01 Å2 / CC1/2: 0.939 / Net I/σ(I): 9.1
Reflection shellResolution: 4.79→5.64 Å / Num. unique obs: 398 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 4.79→39.72 Å / SU ML: 0.8595 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 43.0645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2892 115 5.31 %
Rwork0.2454 2050 -
obs0.2476 2165 59.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 264.65 Å2
Refinement stepCycle: LAST / Resolution: 4.79→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 2 0 858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169956
X-RAY DIFFRACTIONf_angle_d1.49631467
X-RAY DIFFRACTIONf_chiral_restr0.082167
X-RAY DIFFRACTIONf_plane_restr0.010642
X-RAY DIFFRACTIONf_dihedral_angle_d39.7379407
LS refinement shellResolution: 4.79→39.72 Å
RfactorNum. reflection% reflection
Rfree0.2892 115 -
Rwork0.2454 2050 -
obs--59.28 %

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