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

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Basic information

Entry
Database: PDB / ID: 8tap
TitleSequence specific (AATT) orientation of netropsin molecules at a unique minor groove binding site (position2) within a self-assembled 3D DNA lattice (4x6)
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*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*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 / homologyNETROPSIN / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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*CP*AP*GP*AP*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*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2265
Polymers12,7954
Non-polymers4301
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.640, 68.640, 56.538
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*GP*AP*AP*AP*TP*TP*A)-3')


Mass: 6505.238 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*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 , 2 types, 3 molecules

#5: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic*YM
#6: 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: 6.01 Å3/Da / Density % sol: 79.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Na Cacodylate pH 6.0 with 10 mM MgCl2, 2.5 mM spermidine, and 2.5 M NaCl 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: Apr 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 4797 / % possible obs: 89.4 % / Redundancy: 9.2 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Χ2: 0.826 / Net I/σ(I): 5.2 / Num. measured all: 44258
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.155.81.0241420.7510.9260.4141.1120.43752
3.15-3.216.60.3221720.9760.9940.120.3450.70261
3.21-3.276.70.2081790.9930.9980.0730.2211.11567.3
3.27-3.347.20.5061740.950.9870.1880.5420.6570.7
3.34-3.417.60.4062120.9640.9910.1490.4340.66778.5
3.41-3.497.60.52210.9490.9870.180.5330.48382.5
3.49-3.5880.322380.9790.9950.1150.3410.48987.2
3.58-3.687.80.4782570.940.9840.1770.5120.55593.8
3.68-3.788.70.4962540.950.9870.1740.5270.50595.5
3.78-3.919.10.5762510.9350.9830.1990.610.519100
3.91-4.0410.30.4112900.9660.9910.1340.4330.52100
4.04-4.2110.50.2922680.9790.9950.0950.3070.613100
4.21-4.410.50.2562610.9850.9960.0830.270.606100
4.4-4.6310.40.1952710.9920.9980.0630.2050.613100
4.63-4.92100.1722720.9910.9980.0570.1820.674100
4.92-5.310.50.1152640.9910.9980.0370.1210.945100
5.3-5.83110.0882570.9970.9990.0280.0931.046100
5.83-6.6710.70.0792750.9970.9990.0260.0831.061100
6.67-8.410.10.0582640.99810.0190.0611.318100
8.4-5010.50.0592750.99910.0190.0622.144100

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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: 3.11→34.32 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 243 5.1 %
Rwork0.2069 --
obs0.2093 4765 89.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 31 2 888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006988
X-RAY DIFFRACTIONf_angle_d0.921511
X-RAY DIFFRACTIONf_dihedral_angle_d35.255417
X-RAY DIFFRACTIONf_chiral_restr0.045166
X-RAY DIFFRACTIONf_plane_restr0.00549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.910.32141060.29691967X-RAY DIFFRACTION78
3.92-34.320.23741370.18632555X-RAY DIFFRACTION100

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