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- PDB-8tam: Sequence specific (AATT) orientation of Hoechst molecules at two ... -

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Basic information

Entry
Database: PDB / ID: 8tam
TitleSequence specific (AATT) orientation of Hoechst molecules at two unique minor groove binding sites within a self-assembled 3D DNA lattice (4x6)
Components
  • DNA (5'-D(*GP*AP*GP*AP*AP*TP*TP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*AP*TP*TP*A)-3')
  • DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*T)-3')
  • DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3')
  • DNA (5'-D(P*GP*GP*AP*AP*TP*TP*C)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice / Minor Groove Binders / Netropsin / DAPI / Hoechst / ImPyPy / polyamide / host-guest
Function / homology: / Chem-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 27, 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*AP*AP*TP*TP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*AP*TP*TP*A)-3')
B: DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*T)-3')
D: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8168
Polymers12,7934
Non-polymers1,0234
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.488, 116.488, 49.299
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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*AP*AP*TP*TP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*AP*TP*TP*A)-3')


Mass: 6495.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3')


Mass: 1769.193 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*T)-3')


Mass: 2391.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*GP*AP*AP*TP*TP*C)-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, 8 molecules

#5: Chemical ChemComp-HT1 / 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33342 / Bisbenzimide


Mass: 452.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H28N6O
#6: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.03 Å3/Da / Density % sol: 75.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M TRIS pH 8.0 with 10 mM MgCl2, 1.0 mM CoH18N6, and 20% 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: Dec 18, 2021
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: 5263 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.019 / Rrim(I) all: 0.061 / Χ2: 0.825 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.95-38.71.1532720.8220.950.4021.2230.41199.3
3-3.0690.7362550.9440.9860.2530.7790.443100
3.06-3.118.90.4972720.9730.9930.1740.5270.444100
3.11-3.189.40.3042470.9930.9980.1040.3220.508100
3.18-3.259.70.1312780.99810.0450.1380.647100
3.25-3.3210.50.0842650.99910.0270.0880.863100
3.32-3.4110.60.1062520.99810.0340.1110.74100
3.41-3.510.50.1092670.9980.9990.0350.1140.771100
3.5-3.610.40.1152560.9970.9990.0370.1210.698100
3.6-3.7210.20.1132700.9960.9990.0370.1190.629100
3.72-3.859.70.0932640.9960.9990.0320.0990.83100
3.85-410.10.0782560.9970.9990.0260.0820.945100
4-4.1910.40.0722620.9970.9990.0230.0760.991100
4.19-4.4110.70.0722720.9980.9990.0230.0761.005100
4.41-4.6810.70.0642620.9980.9990.020.0671.02100
4.68-5.04100.0512670.99910.0170.0530.957100
5.04-5.5510.30.0452550.99910.0150.0481.049100
5.55-6.3510.90.0422670.99910.0130.0440.925100
6.35-89.90.0382570.99910.0130.040.873100
8-5010.50.0482670.9970.9990.0150.0511.502100

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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→44.29 Å / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 266 5.12 %
Rwork0.2212 --
obs0.2217 5199 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 70 4 929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051034
X-RAY DIFFRACTIONf_angle_d0.9251579
X-RAY DIFFRACTIONf_dihedral_angle_d33.383422
X-RAY DIFFRACTIONf_chiral_restr0.032166
X-RAY DIFFRACTIONf_plane_restr0.00448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.710.30221330.28982438X-RAY DIFFRACTION97
3.72-44.290.21031330.20282495X-RAY DIFFRACTION100

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