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- PDB-8dxz: [T:Au+:T--(pH11-pH7; 420s)] Metal-mediated DNA base pair in tense... -

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Basic information

Entry
Database: PDB / ID: 8dxz
Title[T:Au+:T--(pH11-pH7; 420s)] Metal-mediated DNA base pair in tensegrity triangle grown at pH 11 and soaked in pH 7 for 420s
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: 4.71 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: To Be Published
Title: Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs
Authors: Lu, B. / Ohayon, Y.P. / Sha, R. / Woloszyn, K. / Rothschild, L. / Wind, S. / Hendrickson, W. / Mao, C. / Seeman, N.C. / Vecchioni, S.
History
DepositionAug 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 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*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)12,9845
Polymers12,7874
Non-polymers1971
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)38,95315
Polymers38,36212
Non-polymers5913
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)106.037, 106.037, 94.980
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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / 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: 8.04 Å3/Da / Density % sol: 84.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 11
Details: 40 mM Tris, 125 mM magnesium sulfate, 12 uM gold(I) phosphine
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: Jul 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 4.71→66.02 Å / Num. obs: 3146 / % possible obs: 87.2 % / Redundancy: 10.8 % / Biso Wilson estimate: 249.6 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.4
Reflection shellResolution: 4.71→5.24 Å / Num. unique obs: 402 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 4.71→33.01 Å / SU ML: 0.6333 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.7657
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1581 150 4.84 %
Rwork0.1506 2947 -
obs0.1522 3097 75.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 251.44 Å2
Refinement stepCycle: LAST / Resolution: 4.71→33.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 1 0 859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178958
X-RAY DIFFRACTIONf_angle_d1.52821471
X-RAY DIFFRACTIONf_chiral_restr0.0864167
X-RAY DIFFRACTIONf_plane_restr0.00942
X-RAY DIFFRACTIONf_dihedral_angle_d39.1623407
LS refinement shellResolution: 4.71→33.01 Å
RfactorNum. reflection% reflection
Rfree0.1581 150 -
Rwork0.1506 2947 -
obs--75.13 %
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)
12.89637861527-2.082765144940.8731656100118.43171500536-0.9093540491584.25601219142-0.319205028041.332789828241.86083257782-1.20732784878-1.058505256380.6915804172141.82724805918-0.4725867162391.380598588293.319126645010.1405997471810.2133113303081.816759102140.4692483042492.72734110591-17.701318784518.8101347863-1.22148686469
25.28888344547-1.686197256382.507097040496.26050534724-2.70369388832.687397474752.51109698716-0.328095770491-0.884205433429-0.883439124729-0.1119740689550.0545202048795-3.336275042151.48876810748-0.5591883707093.32758043824-0.2202976553120.4462183318421.11218178391-0.1368600999612.19599613173-9.48849585541-1.8305455223511.3540176782
33.3082624155-0.198266148219-1.783688616025.648670393061.129584984092.131733193560.657888078490.106912435290.4839032916960.601295951980.3736457749320.4028092732190.630885534391-0.8892444178180.5806816008032.437477279930.104831769773-0.1141510425721.47937353861.462195639142.99104839539-15.8963222011-18.934474081117.1045543018
48.571184355250.945293159745-7.987584872215.11587977016-0.7010225629337.40465357641.649662335980.5445965673011.121995218131.06400270091.335661346641.40422380725-0.901606217286-1.883160990681.889851637791.858746270030.0948909792149-0.4805069157381.650525460041.148933701891.72617651028-14.27038612280.2290342964058.45097894857
51.78770733414-0.1780392421191.973163141183.00722902096-0.8879280894184.70647874418-0.512198754364-0.7258742299540.546709259057-0.4272883230762.30767745034-0.4684178357691.03661109577-1.26692742226-1.107401014922.463651712680.125479801078-0.676350614462.160704104290.697460921512.95344644055-17.126825287820.2938282007-5.24485812047
62.902427143914.20822591081.050472140646.343262692920.8018889199833.18220441488-0.664207711705-0.7295849273850.5739303289483.030920803640.317333719085-0.1074724953310.0954101574475-0.460920571205-2.697927921012.973204444360.0310813083707-0.4531664192921.440573882431.033233497492.32318068063-13.2675351571-19.647271665822.3401074342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 15 )AA11 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 21 )AA16 - 21
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )BB1 - 7
5X-RAY DIFFRACTION5chain 'C' and (resid 8 through 14 )CC8 - 14
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 7 )DD1 - 7

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