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- PDB-7sd8: [U:Hg2+:U] Metal-mediated DNA base pair in a self-assembling rhom... -

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Basic information

Entry
Database: PDB / ID: 7sd8
Title[U:Hg2+:U] 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*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*UP*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 / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 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 19, 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*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*UP*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)14,3666
Polymers13,9654
Non-polymers4012
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*UP*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*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*UP*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*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*UP*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)43,09918
Polymers41,89512
Non-polymers1,2046
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)106.284, 106.284, 93.516
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*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6449.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*UP*AP*CP*A)-3')


Mass: 3258.137 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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / 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: 7.28 Å3/Da / Density % sol: 83.1 % / 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: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 2.94→65.599 Å / Num. obs: 4559 / % possible obs: 74.1 % / Redundancy: 11.2 % / Biso Wilson estimate: 102.92 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.94-3.289.61.32290.7341
9.702-65.5999.638.32280.994199.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.94→32.8 Å / SU ML: 0.3395 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 43.0007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 463 10.22 %
Rwork0.2025 4068 -
obs0.204 4531 54.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 167.82 Å2
Refinement stepCycle: LAST / Resolution: 2.94→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 776 82 0 858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087956
X-RAY DIFFRACTIONf_angle_d1.08971467
X-RAY DIFFRACTIONf_chiral_restr0.0545167
X-RAY DIFFRACTIONf_plane_restr0.005542
X-RAY DIFFRACTIONf_dihedral_angle_d37.6724407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.370.2435290.2537259X-RAY DIFFRACTION10.37
3.37-4.240.35391560.33511334X-RAY DIFFRACTION53.71
4.24-32.80.19732780.18322475X-RAY DIFFRACTION98.78
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)
10.73505090766-0.0844631130319-0.3713833543581.83442814703-0.10121937688-0.006553497566820.8869869126810.153737535257-0.140848339672-0.690176370161-0.20436435124-0.340147401055-0.351479533448-0.3746740633210.002572053189521.770553198960.2513551482110.4778085755981.7154634453-0.3162543006511.5725009763810.08411.616-23.055
20.234929466284-0.0124716359356-0.396914709316-0.000569830311756-0.006806440450540.6765061088451.78026265361-1.112457536741.112686140960.01688049884660.304143596016-0.324081662878-1.498418788861.032115420480.0973513751.417154103310.1010013049970.2961195883041.55475469374-0.4389551069681.546059119847.29412.252-21.415
31.21975890788-0.8856448087262.258323208151.08478769633-2.053298314894.543861476471.45825637898-0.4141596854250.518237375195-0.4899483307520.3430426946120.337956794332-0.947493249118-0.7560679468540.730804430631.307975046960.1919164833860.5979169513831.35324514419-0.2971336417651.5075893011125.8494.583-35.246
40.333100435899-0.6175679058450.03655196890892.82055312588-0.965517819010.499766463280.152172483723-1.90362428497-0.7822403694270.503531479727-0.766773263665-0.00130876926006-0.2976930122780.4822261590270.2023835323621.342508437260.3441685447170.7896329161722.005661499330.2168926619851.43362919995-10.47121.516-8.076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:21 )A1 - 21
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:11 )B1 - 11
3X-RAY DIFFRACTION3( CHAIN C AND RESID 8:14 )C8 - 14
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:7 )D1 - 7

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