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

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Basic information

Entry
Database: PDB / ID: 8tbd
TitleSequence specific (AATT) orientation of Hoechst molecules at a unique minor groove binding site (position2) within a self-assembled 3D DNA lattice (4x5)
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*AP*TP*TP*A)-3')
  • DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*GP*T*(HT1))-3')
  • DNA (5'-D(P*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice / Minor Groove Binders / Netropsin / DAPI / Hoechst / ImPyPy / polyamide / host-guest
Function / homologyCACODYLATE ION / Chem-HT1 / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*AP*CP*AP*AP*TP*TP*A)-3')
B: DNA (5'-D(P*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*GP*T*(HT1))-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,82010
Polymers12,7954
Non-polymers1,0256
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.345, 68.345, 58.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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DNA chain , 4 types, 4 molecules ABCD

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


Mass: 6465.213 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*AP*AP*TP*TP*GP*T*(HT1))-3')


Mass: 2720.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 9 molecules

#5: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 6.15 Å3/Da / Density % sol: 80.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Na Cacodylate pH 6.0 with 200 mM MgCl2 and 2.5 M KCl 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: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 5544 / % possible obs: 91.1 % / Redundancy: 9.6 % / CC1/2: 0.899 / CC star: 0.973 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.037 / Rrim(I) all: 0.122 / Χ2: 1.228 / Net I/σ(I): 8.4 / Num. measured all: 53271
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3-3.058.11.1441710.7420.9230.4111.2190.41559.8
3.05-3.118.20.4332050.9710.9930.1550.4610.47263.3
3.11-3.177.50.1352000.9970.9990.0480.1430.70269.2
3.17-3.238.50.092360.99810.0290.0941.28375.2
3.23-3.38.30.0972480.99810.0320.1020.80383.2
3.3-3.388.90.1952760.9940.9990.0670.2070.58389
3.38-3.469.30.1472910.9980.9990.0490.1550.67390.4
3.46-3.569.30.1212760.9980.9990.040.1280.83796.2
3.56-3.669.30.1912800.9960.9990.0640.2010.62196.2
3.66-3.789.50.4993240.9910.9980.1960.5360.9699.7
3.78-3.918.70.1422970.9960.9990.0490.150.73599.7
3.91-4.0710.70.1373030.9970.9990.0440.1440.808100
4.07-4.2610.60.1183160.9970.9990.0380.1240.81100
4.26-4.4810.70.122970.9970.9990.0380.1260.852100
4.48-4.7610.50.0973020.9970.9990.0310.1020.871100
4.76-5.139.60.0773040.9970.9990.0260.0821.15599.7
5.13-5.6410.70.0713100.99810.0230.0741.515100
5.64-6.4610.80.0672990.9970.9990.0210.0711.408100
6.46-8.139.90.0553060.99910.0180.0581.82999.7
8.13-5010.50.1233030.9940.9990.0380.1295.45199.7

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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: 3→41.57 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 43.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 328 6.09 %
Rwork0.2448 --
obs0.2467 5389 88.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 853 39 3 895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005993
X-RAY DIFFRACTIONf_angle_d0.8471521
X-RAY DIFFRACTIONf_dihedral_angle_d34.249412
X-RAY DIFFRACTIONf_chiral_restr0.037166
X-RAY DIFFRACTIONf_plane_restr0.00445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.780.39961360.40322229X-RAY DIFFRACTION78
3.79-41.570.23831920.2092832X-RAY DIFFRACTION100

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