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- PDB-8tc6: Sequence specific (AATT and TGTCA) orientation of netropsin and I... -

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Basic information

Entry
Database: PDB / ID: 8tc6
TitleSequence specific (AATT and TGTCA) orientation of netropsin and ImPyPy 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*TP*GP*TP*CP*AP*C*(NT))-3')
  • DNA (5'-D(*TP*CP*GP*TP*GP*AP*CP*AP*T)-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 / homologyCACODYLATE ION / NETROPSIN / Chem-ZQQ / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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*TP*GP*TP*CP*AP*C*(NT))-3')
B: DNA (5'-D(P*CP*GP*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*GP*TP*GP*AP*CP*AP*T)-3')
D: DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5539
Polymers12,7974
Non-polymers1,7565
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.921, 67.921, 65.476
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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*TP*GP*TP*CP*AP*C*(NT))-3')


Mass: 6457.187 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*GP*TP*GP*AP*CP*AP*T)-3')


Mass: 2730.810 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 , 4 types, 9 molecules

#5: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic*YM
#6: Chemical ChemComp-ZQQ / N-[5-({5-[(3-{[3-(dimethylamino)propyl]amino}-3-oxopropyl)carbamoyl]-1-methyl-1H-pyrrol-3-yl}carbamoyl)-1-methyl-1H-pyrrol-3-yl]-1-methyl-1H-imidazole-2-carboxamide


Mass: 525.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H35N9O4
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M Na cacodylate pH 7.0 with 9 mM MgCl2, 2.25 mM spermine, 1.8 mM CoH18N6, 0.9 mM spermidine, and 5% PEG 400 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 6739 / % possible obs: 100 % / Redundancy: 18.6 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.016 / Rrim(I) all: 0.066 / Χ2: 1.902 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.45-2.4916.61.3963280.7810.9370.3461.4390.271100
2.49-2.5417.41.1183320.8650.9630.271.1510.33100
2.54-2.5918.30.973260.9290.9820.230.9970.29100
2.59-2.6418.70.8793230.9360.9830.2070.9030.295100
2.64-2.718.90.5943430.9750.9940.1390.610.313100
2.7-2.76190.5453160.9670.9920.1280.5610.329100
2.76-2.8318.80.3893330.9850.9960.0920.40.347100
2.83-2.917.60.3433220.9830.9960.0840.3530.456100
2.9-2.9917.60.2363450.9960.9990.0570.2430.402100
2.99-3.0919.30.1723310.9980.9990.040.1770.414100
3.09-3.218.20.0893350.99910.0210.0921.013100
3.2-3.3217.80.0783210.99910.020.0812.102100
3.32-3.4820.40.063346110.0140.0640.629100
3.48-3.6620.50.0573400.99910.0130.0591.524100
3.66-3.8920.40.0673330.9950.9990.0150.0693.045100
3.89-4.1920.10.0593460.9980.9990.0130.062.728100
4.19-4.6119.40.0563350.9980.9990.0130.0575100
4.61-5.2817.90.0543480.9980.9990.0130.0554.488100
5.28-6.6517.40.053550.9970.9990.0120.0515.009100
6.65-5017.10.0483810.9910.9980.0150.0518.15299.7

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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: 2.45→43.76 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 47.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 330 4.99 %
Rwork0.2721 --
obs0.2732 6614 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 109 4 968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061068
X-RAY DIFFRACTIONf_angle_d0.8341621
X-RAY DIFFRACTIONf_dihedral_angle_d35.703437
X-RAY DIFFRACTIONf_chiral_restr0.04166
X-RAY DIFFRACTIONf_plane_restr0.00463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-3.080.44351610.49333107X-RAY DIFFRACTION99
3.08-43.760.27311690.23863177X-RAY DIFFRACTION98

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