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- PDB-6wk7: Crystal Structure Analysis of a poly(thymine) DNA duplex -

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Basic information

Entry
Database: PDB / ID: 6wk7
TitleCrystal Structure Analysis of a poly(thymine) DNA duplex
ComponentsDNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
KeywordsDNA / melamine-mediated / poly(thymine) DNA duplex
Function / homology1,3,5-triazine-2,4,6-triamine / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.423 Å
AuthorsLi, Q. / Zhao, J. / Liu, L. / Mandal, S. / Rizzuto, F.J. / He, H. / Wei, S. / Jonchhe, S. / Sleiman, H.F. / Mao, H. / Mao, C.
Funding support China, United States, Canada, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21974111 China
National Science Foundation (NSF, United States)CBET-1904921 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NIH 1R01CA236350 United States
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Office of Naval ResearchN00014-15-1-2707 United States
Banting Postdoctoral Fellowships Canada
Canada Research Chairs Canada
CitationJournal: Nat Mater / Year: 2020
Title: A poly(thymine)-melamine duplex for the assembly of DNA nanomaterials.
Authors: Li, Q. / Zhao, J. / Liu, L. / Jonchhe, S. / Rizzuto, F.J. / Mandal, S. / He, H. / Wei, S. / Sleiman, H.F. / Mao, H. / Mao, C.
History
DepositionApr 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
C: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3178
Polymers3,5602
Non-polymers7576
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area2760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.665, 67.665, 67.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')


Mass: 1780.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AX2 / 1,3,5-triazine-2,4,6-triamine / Melamine


Mass: 126.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H6N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.63 Å3/Da / Density % sol: 66.07 % / Description: Cubic-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: magnesium chloride hexahydrate, MOPS, ammonium sulfate, spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 2064 / % possible obs: 99.3 % / Redundancy: 10.7 % / Biso Wilson estimate: 44.13 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Χ2: 0.973 / Net I/σ(I): 10.9 / Num. measured all: 22011
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.42-2.469.60.362890.9490.120.3820.86288.1
2.46-2.5110.70.3511090.9520.1120.3680.851100
2.51-2.5510.80.366970.9470.1170.3840.947100
2.55-2.61110.3171000.9730.0990.3320.994100
2.61-2.6610.60.2721040.9720.0870.2860.932100
2.66-2.7310.80.32970.9690.1020.3361.078100
2.73-2.7910.90.21050.9850.0630.210.922100
2.79-2.8710.90.2391010.9890.0750.250.987100
2.87-2.95110.1631070.9930.0510.1710.923100
2.95-3.0510.90.1221000.9970.0390.1280.931100
3.05-3.1610.90.075940.9980.0240.0790.984100
3.16-3.2810.70.02911310.010.0310.948100
3.28-3.4310.70.03610210.0110.0380.969100
3.43-3.6110.80.0419810.0130.0421.161100
3.61-3.8410.70.0691050.9980.0220.0731.192100
3.84-4.1410.70.0621050.9990.020.0661.096100
4.14-4.5510.80.0371080.9990.0120.0390.957100
4.55-5.2110.50.03910510.0130.0410.91100
5.21-6.5610.70.03210610.010.0340.935100
6.56-509.60.02411910.0080.0260.87898.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER1.12phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d3x

1d3x


Resolution: 2.423→27.624 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 24.03
RfactorNum. reflection% reflection
Rfree0.2625 204 9.95 %
Rwork0.2275 --
obs0.2311 2051 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.76 Å2 / Biso mean: 45.4515 Å2 / Biso min: 21.47 Å2
Refinement stepCycle: final / Resolution: 2.423→27.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 234 54 29 317
Biso mean--34.4 56.32 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011314
X-RAY DIFFRACTIONf_angle_d1.288470
X-RAY DIFFRACTIONf_chiral_restr0.06146
X-RAY DIFFRACTIONf_plane_restr0.00618
X-RAY DIFFRACTIONf_dihedral_angle_d37.467112
LS refinement shellResolution: 2.423→27.624 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2625 204 -
Rwork0.2275 1847 -
obs--99 %
Refinement TLS params.Method: refined / Origin x: 5.7765 Å / Origin y: 40.3085 Å / Origin z: 16.5784 Å
111213212223313233
T0.3295 Å20.1156 Å20.1389 Å2-0.3325 Å2-0.015 Å2--0.3888 Å2
L0.215 °20.1596 °20.3211 °2-0.3325 °20.0833 °2--0.5958 °2
S0.4601 Å °0.2622 Å °0.987 Å °-0 Å °-0.0867 Å °-0.1982 Å °-0.0825 Å °-0.032 Å °0.2007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 6
2X-RAY DIFFRACTION1allC1 - 6
3X-RAY DIFFRACTION1allD1 - 5
4X-RAY DIFFRACTION1allD6
5X-RAY DIFFRACTION1allG1 - 29

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