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- PDB-8ta8: Sequence specific (AATT) orientation of netropsin molecules at tw... -

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Basic information

Entry
Database: PDB / ID: 8ta8
TitleSequence specific (AATT) orientation of netropsin 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*(NT)*(NT))-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 / homologyNETROPSIN / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 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 26, 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*(NT)*(NT))-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)13,6546
Polymers12,7934
Non-polymers8612
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-9 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.477, 68.477, 58.254
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*AP*AP*TP*TP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*AP*TP*TP*A*(NT)*(NT))-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 , 2 types, 4 molecules

#5: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 2 / 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: 6.16 Å3/Da / Density % sol: 80.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Tris pH 7.5 with 200 mM MgCl2 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: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 5425 / % possible obs: 93.2 % / Redundancy: 10 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.017 / Rrim(I) all: 0.055 / Χ2: 0.805 / Net I/σ(I): 8.2 / Num. measured all: 53988
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.05-3.18.30.7382300.9220.980.2630.7850.44274.4
3.1-3.168.80.2492000.9950.9990.0860.2640.58172.5
3.16-3.228.90.1332270.9970.9990.0450.141.0274.2
3.22-3.2990.112340.9970.9990.0370.1171.33181.5
3.29-3.368.70.1892370.9950.9990.0650.20.70684.9
3.36-3.439.60.1512600.9970.9990.050.1590.84689
3.43-3.529.80.1572530.9950.9990.0520.1660.78890
3.52-3.629.40.1432950.9970.9990.0490.1520.77297.7
3.62-3.7210.20.1872840.990.9970.0620.1970.77299.3
3.72-3.8410.30.1492910.9970.9990.0480.1570.728100
3.84-3.9810.50.1453000.9980.9990.0460.1520.732100
3.98-4.149.90.1122940.99910.0380.1180.761100
4.14-4.3310.20.1012810.99810.0330.1060.736100
4.33-4.5610.50.0912950.9980.9990.0290.0950.739100
4.56-4.8411.20.0792850.9970.9990.0250.0830.765100
4.84-5.2110.90.0612890.99910.0190.0640.788100
5.21-5.7410.50.052990.99910.0160.0530.867100
5.74-6.579.70.0462850.99910.0150.0480.786100
6.57-8.27110.036296110.0110.0380.848100
8.27-5010.30.0382900.99910.0120.041.054100

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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: 3.05→41.56 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 34.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2426 261 4.92 %
Rwork0.2146 --
obs0.2162 5301 91.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 62 2 919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061020
X-RAY DIFFRACTIONf_angle_d0.861555
X-RAY DIFFRACTIONf_dihedral_angle_d34.907428
X-RAY DIFFRACTIONf_chiral_restr0.042166
X-RAY DIFFRACTIONf_plane_restr0.00556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.840.29131250.29222279X-RAY DIFFRACTION83
3.85-41.560.22761360.19572761X-RAY DIFFRACTION100

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