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- PDB-8tb8: Sequence specific (AATT) orientation of Hoechst molecules at a un... -

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Basic information

Entry
Database: PDB / ID: 8tb8
TitleSequence specific (AATT) orientation of Hoechst molecules at a unique minor groove binding site (position1) within a self-assembled 3D DNA lattice (4x5)
Components
  • DNA (5'-D(*GP*AP*CP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A*(HT1))-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*CP*AP*AP*TP*TP*G)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice / Minor Groove Binders / Netropsin / DAPI / Hoechst / ImPyPy / polyamide / host-guest
Function / homologyChem-HT1 / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSimmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1360635 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104960 United States
National Science Foundation (NSF, United States)NSF2004250 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals.
Authors: Simmons, C.R. / Buchberger, A. / Henry, S.J.W. / Novacek, A. / Fahmi, N.E. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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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*CP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A*(HT1))-3')
B: DNA (5'-D(P*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')
D: DNA (5'-D(P*GP*CP*AP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2726
Polymers12,7954
Non-polymers4772
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.195, 68.195, 60.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-201-

HOH

21C-202-

HOH

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Components

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DNA chain , 4 types, 4 molecules ABCD

#1: DNA chain DNA (5'-D(*GP*AP*CP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*GP*AP*CP*AP*CP*TP*CP*A*(HT1))-3')


Mass: 6416.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*GP*TP*CP*A)-3')


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*T)-3')


Mass: 2761.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*AP*AP*TP*TP*G)-3')


Mass: 2137.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-HT1 / 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33342


Mass: 452.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N6O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M TRIS pH 8.0 with 200 mM MgCl2 and 15% ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Temp details: temperature gradient generated from 60 to 25 C at 0.3 degrees per hour

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 3640 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.018 / Rrim(I) all: 0.073 / Χ2: 0.837 / Net I/σ(I): 8.8 / Num. measured all: 67168
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.95-317.31.3571670.8620.9620.3291.3980.416
3-3.0617.60.921790.9570.9890.2210.9470.452
3.06-3.1117.40.4451840.9930.9980.1090.4580.498
3.11-3.1818.60.2451680.9970.9990.0570.2510.558
3.18-3.2518.40.1371930.99810.0320.1410.843
3.25-3.32200.1561690.99910.0350.160.738
3.32-3.4119.80.1181820.99910.0260.1210.847
3.41-3.519.50.1311700.99810.030.1340.724
3.5-3.619.40.1311880.99910.030.1340.692
3.6-3.7218.40.1381660.9970.9990.0330.1420.661
3.72-3.8517.50.1491810.9980.9990.0360.1540.736
3.85-418.30.1061880.99810.0250.1090.748
4-4.1919.40.0811740.99810.0190.0830.841
4.19-4.4119.30.0781860.99910.0180.080.856
4.41-4.6819.30.0711770.99910.0160.0730.861
4.68-5.0418.30.0611900.99910.0150.0620.906
5.04-5.5518.50.0481840.99910.0120.051.044
5.55-6.3519.10.047185110.0110.0491.096
6.35-817.20.0431940.99910.0110.0451.099
8-5016.30.047215110.0140.0491.947

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→42.32 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 171 4.77 %
Rwork0.2352 --
obs0.2369 3583 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 35 2 892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004995
X-RAY DIFFRACTIONf_angle_d0.7911523
X-RAY DIFFRACTIONf_dihedral_angle_d33.664414
X-RAY DIFFRACTIONf_chiral_restr0.03166
X-RAY DIFFRACTIONf_plane_restr0.00345
LS refinement shellResolution: 2.95→42.32 Å
RfactorNum. reflection% reflection
Rfree0.2718 171 -
Rwork0.2352 3412 -
obs--99 %

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