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- PDB-8tb4: Sequence specific (AATT) orientation of DAPI molecules at a uniqu... -

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Basic information

Entry
Database: PDB / ID: 8tb4
TitleSequence specific (AATT) orientation of DAPI molecules at a unique minor groove binding site (position2) 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*GP*T*(DAP))-3')
  • DNA (5'-D(P*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 / homology6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / 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 28, 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*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*AP*AP*TP*TP*GP*T*(DAP))-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1468
Polymers12,7954
Non-polymers3504
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.507, 69.507, 59.552
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*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*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*AP*AP*TP*TP*GP*T*(DAP))-3')


Mass: 2720.808 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, 4 molecules

#5: Chemical ChemComp-DAP / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 6.49 Å3/Da / Density % sol: 81.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M HEPES pH 7.5 with 15 mM MgCl2, 1.0 mM spermidine, and 10% dioxan 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: APS / Beamline: 19-ID / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 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: 5774 / % possible obs: 99.7 % / Redundancy: 9.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.042 / Rrim(I) all: 0.136 / Χ2: 4.546 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.156.71.6292910.6440.8850.6271.7550.4597.3
3.15-3.217.60.4822690.9650.9910.1780.5160.5498.2
3.21-3.2780.2563060.9920.9980.0890.2710.763100
3.27-3.349.10.2172940.9960.9990.0730.2290.793100
3.34-3.419.30.6652580.9390.9840.2280.7030.465100
3.41-3.499.80.412980.9770.9940.1370.4320.575100
3.49-3.589.70.5512990.9740.9930.1840.5810.77100
3.58-3.689.30.5342940.910.9760.1850.5652.272100
3.68-3.789.50.7582770.9260.9810.2580.8020.92999.6
3.78-3.9110.80.2772970.980.9950.0880.290.753100
3.91-4.0410.60.2192880.9890.9970.070.230.748100
4.04-4.2110.70.1732900.9890.9970.0550.1820.852100
4.21-4.410.50.1542890.9920.9980.050.1621.002100
4.4-4.6310.40.1352860.9930.9980.0440.1421.075100
4.63-4.929.30.112920.9870.9970.0380.1173.02299.3
4.92-5.310.70.0982830.9810.9950.0310.1034.002100
5.3-5.8310.70.0852970.9820.9960.0270.094.967100
5.83-6.6710.50.0762810.9860.9970.0240.0795.661100
6.67-8.4100.0672950.9760.9940.0220.077.27299.7
8.4-5010.40.1322900.9840.9960.0430.13948.164100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→42.37 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / SU B: 20.035 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23789 304 5.4 %RANDOM
Rwork0.19501 ---
obs0.19728 5335 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 138.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 3.11→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 24 0 879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.011979
X-RAY DIFFRACTIONr_bond_other_d0.0680.017485
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.7911500
X-RAY DIFFRACTIONr_angle_other_deg1.6471.5441147
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_restr0.1460.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02157
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_it14.66314.072979
X-RAY DIFFRACTIONr_scbond_other14.65614.074980
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.04421.0371501
X-RAY DIFFRACTIONr_long_range_B_refined24.0441477
X-RAY DIFFRACTIONr_long_range_B_other24.0371478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.11→3.188 Å
RfactorNum. reflection% reflection
Rfree0.528 15 -
Rwork0.347 360 -
obs--86.41 %

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