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- PDB-7ti3: [T:Hg2+:T--pH 11] Metal-mediated DNA base pair in tensegrity triangle -

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Basic information

Entry
Database: PDB / ID: 7ti3
Title[T:Hg2+:T--pH 11] Metal-mediated DNA base pair in tensegrity triangle
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*TP*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: 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
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 30, 2023Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_audit_support.country

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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*TP*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*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)13,1896
Polymers12,7874
Non-polymers4012
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*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*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*TP*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*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*TP*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*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)39,56618
Polymers38,36212
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)106.694, 106.694, 88.189
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*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6463.185 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*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

CrystalDescription: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11 / Details: Tris, 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: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 4.79→39.8 Å / Num. obs: 2474 / % possible obs: 83.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 256.53 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.7
Reflection shellResolution: 4.79→5.6 Å / Num. unique obs: 414 / CC1/2: 0.415

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 4.79→39.8 Å / SU ML: 0.6713 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 123 5.43 %
Rwork0.169 2144 -
obs0.1716 2267 61.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.35 Å2
Refinement stepCycle: LAST / Resolution: 4.79→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 2 0 860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012958
X-RAY DIFFRACTIONf_angle_d1.35081471
X-RAY DIFFRACTIONf_chiral_restr0.0683167
X-RAY DIFFRACTIONf_plane_restr0.007842
X-RAY DIFFRACTIONf_dihedral_angle_d39.6601407
LS refinement shellResolution: 4.79→39.8 Å
RfactorNum. reflection% reflection
Rfree0.2207 123 -
Rwork0.169 2144 -
obs--61.67 %
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)
10.5398725300791.018024518610.4677792068142.025743718180.9516826753780.3664959479850.777900421077-0.384284162957-0.33791946638-0.1068646921530.18340407775-1.06675203527-0.489661248294-0.1884165165320.6351394971710.9806421592220.2262679252090.4490642103750.4321147784840.1739223324951.1785998153610.251190363311.5302484334-21.5692762708
20.148431328790.2561787079780.138439497860.4391251045110.2294136929360.09308214889920.449147725177-0.266450743012-0.06635885860740.473057102679-0.08583741095070.1532869701070.2865884933650.434133303210.05094807177682.34795340998-0.185852994651-0.6212851864450.635321009068-0.1570954618240.4880696256157.2298913998912.1634073315-20.0042174434
30.116683493495-0.09583574514890.003025663905830.35828305964-0.01750485633560.033570852366-0.0896961227535-0.2298203534610.0518901588787-0.05172563420140.4516138248760.565679339803-0.588866176272-0.165269626901-0.1075058351611.521866187990.2140095441830.3286345737161.892584325230.3100019582531.2627386853626.41921729274.85946553974-33.3792437147
40.198913292650.0309708452032-0.2260902443560.00392982183137-0.02526117001140.2151848573810.142884340068-0.7023151645610.355829191150.09941022772190.04563518710150.126820057387-0.1775399908960.05959709837140.6836113130661.016590126611.58839226231.464924292550.5978788359560.4686907411830.860738451097-10.600351434321.0484229414-6.77923112947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 21)AA1 - 21
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 7)BB1 - 7
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 14)CC8 - 14
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 7)DD1 - 7

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