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- PDB-8eg4: [iU:Ag+:iU] Metal-mediated DNA base pair in a self-assembling rho... -

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Basic information

Entry
Database: PDB / ID: 8eg4
Title[iU:Ag+:iU] 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*(5IU)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*(5IU)P*AP*CP*A*(AG))-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 / MOLECULAR REPLACEMENT / Resolution: 4.18 Å
AuthorsVecchioni, S. / Lu, B. / 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
Citation
Journal: 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.
#1: Journal: 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 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author

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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*(5IU)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5IU)P*AP*CP*A*(AG))-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)13,4485
Polymers13,3404
Non-polymers1081
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*(5IU)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5IU)P*AP*CP*A*(AG))-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*(5IU)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5IU)P*AP*CP*A*(AG))-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*(5IU)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*(5IU)P*AP*CP*A*(AG))-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)40,34515
Polymers40,02112
Non-polymers3243
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)106.343, 106.343, 89.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallH3
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*(5IU)P*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6575.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*(5IU)P*AP*CP*A*(AG))-3')


Mass: 2507.477 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-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag / 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: 7.33 Å3/Da / Density % sol: 83.22 % / Description: Rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM MOPS, 1.25 M magnesium sulfate, 720 uM silver nitrate
Temp details: 338-293K at 0.4K/hr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0073 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0073 Å / Relative weight: 1
ReflectionResolution: 4.18→64.307 Å / Num. obs: 3757 / % possible obs: 86.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 274.65 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
4.181-4.662112070.3711
9.982-64.30710.52080.9971

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GBI

3gbi


Resolution: 4.18→40.98 Å / SU ML: 0.8741 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 54.9711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3544 238 6.33 %
Rwork0.2871 3519 -
obs0.2907 3757 66.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 311.05 Å2
Refinement stepCycle: LAST / Resolution: 4.18→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 1 0 859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051958
X-RAY DIFFRACTIONf_angle_d0.81231471
X-RAY DIFFRACTIONf_chiral_restr0.039165
X-RAY DIFFRACTIONf_plane_restr0.003442
X-RAY DIFFRACTIONf_dihedral_angle_d37.7189399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.18-5.250.4099760.44881055X-RAY DIFFRACTION39.91
5.27-40.980.34761620.27272464X-RAY DIFFRACTION93.85
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)
12.5340580825-2.271935321831.335678942122.02186158993-0.6178602431211.985642204431.76210850482.79510624363-1.451053601180.05323589290651.30596724541-1.172705502540.345042782183-0.138965010027-2.593295172022.898408838440.0142241032441-0.4558814017783.262834525640.5480170761723.817363743384.227-14.5055.622
24.392328316250.335335557366-0.0087984771492.435556697350.3381810102670.01299840640290.574932602468-0.0951684203367-0.1628788706920.6758407284521.77995251589-0.0530968049241.314040496680.01721007922897.295077270243.578254540040.965858608557-2.697269795550.1591613001044.33529344390.1878631032246.296-12.6776.834
32.036960377080.469076930908-2.002973551161.57166087357-0.422690982083.223247295853.452491695950.724618109604-3.56920016549-2.30530702323-0.175607538214-0.32266584556-0.1918074776752.01945706522-1.146055261973.1763776399-0.178566507352-0.6111932545783.75552848697-0.4805493633545.41419339068-9.554-25.526-5.832
40.197438542812-0.785137971551-1.09306259477.199113774150.7362302012089.161109443560.442034278353-1.26887377772.355339395481.46255285721-2.18521592411.51356490796-0.0727289117413-0.110647988091-2.212263274371.42502154715-0.807287450833-1.289639529053.47207054535-3.06980840075.8959467817222.655-0.94920.398
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 1:7 )B1 - 7
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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