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- PDB-8tc2: Sequence specific (AATT) orientation of netropsin molecules at tw... -

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Basic information

Entry
Database: PDB / ID: 8tc2
TitleSequence specific (AATT) orientation of netropsin molecules at two unique minor groove binding sites 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*G)-3')
  • DNA (5'-D(P*AP*GP*GP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*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 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*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*TP*CP*GP*TP*C)-3')
C: DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*G)-3')
D: DNA (5'-D(P*AP*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2265
Polymers12,7954
Non-polymers4301
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.752, 68.752, 59.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#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*TP*CP*GP*TP*C)-3')


Mass: 1470.998 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*G)-3')


Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*GP*GP*TP*CP*TP*GP*C)-3')


Mass: 2442.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic*YM
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: 6.38 Å3/Da / Density % sol: 80.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Na Cacodylate pH 6.5 with 100 mM MgCl2, 2.0 mM CoH18N6, and 5% isopropanol) 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 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.05→59.54 Å / Num. obs: 5931 / % possible obs: 99.8 % / Redundancy: 10.1 % / CC1/2: 0.954 / CC star: 0.988 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Rrim(I) all: 0.082 / Χ2: 0.67 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.05-3.18.60.7392870.8540.960.2730.7910.6696.3
3.1-3.168.70.2832730.9910.9980.0990.30.57899.3
3.16-3.229.50.1473110.9960.9990.0490.1550.90499.7
3.22-3.299.90.1143040.99810.0370.120.949100
3.29-3.36100.2492920.9920.9980.0830.2630.517100
3.36-3.43100.1812970.9960.9990.0610.1910.613100
3.43-3.529.40.1592900.9970.9990.0550.1680.675100
3.52-3.6210.10.1643080.9970.9990.0540.1730.637100
3.62-3.72100.1952840.9920.9980.0650.2060.549100
3.72-3.8410.60.1422990.9950.9990.0460.1490.6100
3.84-3.9810.70.1173040.9960.9990.0370.1230.629100
3.98-4.1410.60.0912900.9970.9990.030.0960.618100
4.14-4.3310.70.0843090.9980.9990.0270.0880.567100
4.33-4.569.90.0713040.99810.0240.0740.541100
4.56-4.84100.0572800.99810.0190.060.543100
4.84-5.2110.70.0462990.99910.0150.0480.577100
5.21-5.7410.80.0383090.99910.0120.040.582100
5.74-6.5710.40.0362960.99910.0120.0380.524100
6.57-8.279.90.028303110.0090.0290.539100
8.27-5010.30.0792920.9980.9990.0250.0831.604100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→59.54 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.98 / SU B: 11.63 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21083 270 4.7 %RANDOM
Rwork0.19173 ---
obs0.1926 5535 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 119.897 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.12 Å20 Å2
2---0.23 Å20 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 3.05→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 31 0 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.011988
X-RAY DIFFRACTIONr_bond_other_d0.0070.02501
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.2281511
X-RAY DIFFRACTIONr_angle_other_deg2.12431178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02553
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02230
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it15.93412.321988
X-RAY DIFFRACTIONr_scbond_other15.92612.325989
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other21.43518.4351512
X-RAY DIFFRACTIONr_long_range_B_refined22.8151450
X-RAY DIFFRACTIONr_long_range_B_other22.8081451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.054→3.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 20 -
Rwork0.306 382 -
obs--84.63 %

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