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- PDB-8tbo: Sequence specific (AATT) orientation of netropsin molecules at a ... -

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Basic information

Entry
Database: PDB / ID: 8tbo
TitleSequence specific (AATT) orientation of netropsin 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)-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 / homologyCACODYLATE ION / NETROPSIN / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 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 29, 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)-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)13,7749
Polymers12,7954
Non-polymers9785
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.164, 68.164, 63.053
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

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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)-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, 8 molecules

#5: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic*YM
#6: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: 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: 3.3 Å3/Da / Density % sol: 62.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Na Cacodylate pH 7.0, with 18 mM MgCl2, 2.25 mM spermine, 0.9 mM CoH18N6, and 4.5% MPD 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. obs: 5449 / % possible obs: 99.1 % / Redundancy: 16.7 % / CC1/2: 0.956 / CC star: 0.989 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.023 / Rrim(I) all: 0.089 / Χ2: 3.097 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.64121.2692800.7550.9270.3531.3210.41596.9
2.64-2.6914.10.9662580.8540.960.25110.547100
2.69-2.7416.30.7342690.9440.9860.180.7570.46398.2
2.74-2.817.20.6082580.960.990.1470.6260.474100
2.8-2.86180.5072720.970.9920.1190.5210.49199.3
2.86-2.9318.50.3532650.9810.9950.0830.3630.54999.6
2.93-318.50.2522710.9860.9960.0590.2590.8998.9
3-3.0818.60.1562620.99810.0360.1611.015100
3.08-3.1717.40.1272640.9930.9980.0320.1321.55198.9
3.17-3.2815.90.1142620.9960.9990.0320.1192.05696
3.28-3.39180.1092720.99910.0260.1123.69699.3
3.39-3.53170.1092720.9970.9990.0280.1133.88899.6
3.53-3.6917.60.112730.9980.9990.0270.1134.202100
3.69-3.88190.0992660.9980.9990.0230.1024.25999.6
3.88-4.1318.10.0962710.99810.0240.0995.42499.6
4.13-4.4517.60.0912810.9970.9990.0230.0945.25599.6
4.45-4.8916.60.0822840.9970.9990.0220.0855.18899.3
4.89-5.615.50.0742720.9970.9990.020.0775.84999.6
5.6-7.0513.80.0692920.9980.9990.020.0727.0699.7
7.05-5015.30.0663050.9890.9970.020.0697.85798.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.599→43.093 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 269 4.99 %
Rwork0.2119 --
obs0.2138 5389 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→43.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 35 3 893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01988
X-RAY DIFFRACTIONf_angle_d1.121511
X-RAY DIFFRACTIONf_dihedral_angle_d34.596417
X-RAY DIFFRACTIONf_chiral_restr0.059166
X-RAY DIFFRACTIONf_plane_restr0.00749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-3.2740.36961340.37692491X-RAY DIFFRACTION97
3.274-43.0930.22071350.1852629X-RAY DIFFRACTION99

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