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- PDB-8ta9: Sequence specific (AATT) orientation of DAPI molecules at a uniqu... -

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Basic information

Entry
Database: PDB / ID: 8ta9
TitleSequence specific (AATT) orientation of DAPI molecules at a unique minor groove binding site (position1) 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*CP*TP*CP*A*(DAP))-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*GP*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 / homology: / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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*AP*AP*TP*TP*CP*CP*TP*GP*AP*CP*GP*GP*AP*AP*CP*TP*CP*A*(DAP))-3')
B: DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*GP*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)13,1917
Polymers12,7954
Non-polymers3953
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.395, 68.395, 58.132
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*CP*TP*CP*A*(DAP))-3')


Mass: 6456.199 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*GP*AP*GP*TP*T)-3')


Mass: 2432.614 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, 3 molecules

#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-DAP / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5

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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: 6.14 Å3/Da / Density % sol: 79.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Na cacodylate pH 6.5 with 1.0 mM spermine, 2.0 mM CoH18N6, 30 mM CaCl2, and 2.0 M LiCl 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: 2.8→50 Å / Num. obs: 7272 / % possible obs: 97.2 % / Redundancy: 9.7 % / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.038 / Rrim(I) all: 0.124 / Χ2: 4.085 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.857.81.0882790.730.9190.3821.1560.43576.9
2.85-2.97.41.0522990.7860.9380.3821.1220.44281.9
2.9-2.967.60.6893380.9180.9780.2440.7330.44989.7
2.96-3.0280.5663580.9460.9860.1980.6010.47395.5
3.02-3.088.40.4173660.980.9950.1430.4420.49999.2
3.08-3.1590.1883600.9950.9990.0630.1990.732100
3.15-3.238.90.1064110.9980.9990.0360.1120.989100
3.23-3.329.60.113590.9970.9990.0380.1171.048100
3.32-3.4210.70.1063840.9980.9990.0330.1111.343100
3.42-3.5310.60.1163690.9970.9990.0370.1221.516100
3.53-3.6510.70.123670.9970.9990.0380.1261.409100
3.65-3.810.60.1333720.9930.9980.0420.1391.743100
3.8-3.97100.1343860.9940.9980.0450.1411.77100
3.97-4.1810.10.1173630.9920.9980.0380.1233.241100
4.18-4.4410.90.1183760.9910.9980.0370.1233.855100
4.44-4.7910.70.1213760.9790.9950.0390.1274.549100
4.79-5.27100.13890.990.9970.0330.1054.524100
5.27-6.0310.80.093670.9880.9970.0290.0947.441100
6.03-7.5910.60.0773810.9960.9990.0250.0816.609100
7.59-5010.40.1263720.9940.9990.0410.13330.942100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.52 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / SU B: 12.132 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24397 364 5.1 %RANDOM
Rwork0.19245 ---
obs0.19491 6763 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.909 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.8→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 23 0 878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011979
X-RAY DIFFRACTIONr_bond_other_d0.0070.017485
X-RAY DIFFRACTIONr_angle_refined_deg2.3291.7911500
X-RAY DIFFRACTIONr_angle_other_deg0.4921.5441147
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_restr0.1550.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02532
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_it9.0898.484979
X-RAY DIFFRACTIONr_scbond_other9.0858.484980
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.51412.6981501
X-RAY DIFFRACTIONr_long_range_B_refined14.8891452
X-RAY DIFFRACTIONr_long_range_B_other14.8841453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.634 19 -
Rwork0.706 422 -
obs--79.03 %

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