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- PDB-7sd7: [C:Hg2+:T] Metal-mediated DNA base pair in a self-assembling rhom... -

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Basic information

Entry
Database: PDB / ID: 7sd7
Title[C:Hg2+:T] 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(*TP*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.68 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

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


Theoretical massNumber of molelcules
Total (without water)12,9735
Polymers12,7724
Non-polymers2011
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*TP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*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*TP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*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*TP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,91915
Polymers38,31712
Non-polymers6023
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)105.587, 105.587, 89.084
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*TP*AP*CP*A)-3')


Mass: 2066.401 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*C)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2432.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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
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: 7.48 Å3/Da / Description: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: MOPS, Magnesium sulfate, 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: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 3.599→63.805 Å / Num. obs: 2953 / % possible obs: 87 % / Redundancy: 10.5 % / Biso Wilson estimate: 282.28 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible allMean I/σ(I) obs
3.599-3.8717.81970.13154.9
10.16-63.80510.11960.998110035.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.68→32.22 Å / SU ML: 0.3823 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 48.1109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.275 262 4.57 %
Rwork0.2226 5468 -
obs0.2251 2815 71.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 301.23 Å2
Refinement stepCycle: LAST / Resolution: 3.68→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 853 1 0 854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072953
X-RAY DIFFRACTIONf_angle_d1.03811462
X-RAY DIFFRACTIONf_chiral_restr0.0528166
X-RAY DIFFRACTIONf_plane_restr0.005842
X-RAY DIFFRACTIONf_dihedral_angle_d39.6084406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.68-4.640.5463600.42811780X-RAY DIFFRACTION45.91
4.64-32.220.26672020.21061844X-RAY DIFFRACTION96.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.22741544908-0.05282638305840.4940099042735.07811812186-2.074161087320.863746917131-0.493488141410.361038379764-0.3751946748091.706900029082.832967933512.14533556894-0.5246563326-1.4421101379-2.783304893853.459187543870.1162755625410.1564484039092.804793209280.08655063809762.35598127623-15.0226137169-3.577095582521.3172138003
22.626811821742.99586360433-2.055716612148.71176457274-1.491313760811.880223735951.350599337275.210461628671.778738824640.7184974868280.06043633778522.356788410870.0876669324637-0.830905728444-1.529895688732.64706110203-0.303690745898-0.5587253363253.517575936080.8694263372942.19024169184-14.38524138090.35845670250720.3291193072
35.093439087213.87909742234-4.256031202433.01847580863-3.454075309624.11916774735-4.08381922651-3.62706247708-0.74995008206-1.602322633631.977094412995.120821485410.3745232073011.173039807951.263436404143.854536602080.4992963189540.7696140240432.646619734390.4557006834143.54258997336-16.5127261354-19.455070622631.7247257805
41.995339520356.10315585466-3.303770920467.31944635908-3.342500956061.56766992518-4.28145778356.11463129324-0.0500748418994-7.692357179630.331566822711-4.103400412941.05562387379-0.8424714795331.453182922513.555061548240.05575378781510.320383697263.065665208260.9499392168763.39441107714-12.700821635919.51357420665.94259638818
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 101 through 121)AA101 - 121
2X-RAY DIFFRACTION2(chain 'B' and resid 119 through 125)BB119 - 125
3X-RAY DIFFRACTION3(chain 'C' and resid 209 through 214)CD209 - 214
4X-RAY DIFFRACTION4(chain 'D' and resid 101 through 108)DE101 - 108

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