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- PDB-8epd: Engineering Crystals with Tunable Symmetries from 14- or 16-Base-... -

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Basic information

Entry
Database: PDB / ID: 8epd
TitleEngineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands
Components
  • DNA (5'-D(*CP*GP*AP*CP*G)-3')
  • DNA (5'-D(P*CP*GP*TP*TP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*GP*C)-3')
KeywordsDNA / Four-Fold Rotational Axis / Left-Handed / Parallel
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsZhang, C. / Zhao, J. / Lu, B. / Sha, R. / Seeman, N.C. / Noinaj, N. / Mao, C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CMMI-2025187 United States
National Science Foundation (NSF, United States)CCF-2107393 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions.
Authors: Zhang, C. / Zhao, J. / Lu, B. / Seeman, N.C. / Sha, R. / Noinaj, N. / Mao, C.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: 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 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(P*CP*GP*TP*TP*CP*C)-3')
A: DNA (5'-D(*CP*GP*AP*CP*G)-3')
B: DNA (5'-D(P*GP*GP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8103
Polymers4,8103
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area3530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.166, 34.166, 104.316
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: DNA chain DNA (5'-D(P*CP*GP*TP*TP*CP*C)-3')


Mass: 1760.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*GP*AP*CP*G)-3')


Mass: 1505.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*AP*GP*C)-3')


Mass: 1545.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.5 ug/uL motif 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium pH 7.0, 0.16 M lithium sulfate monohydrate, 4 % MPD at pH 7.0

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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: Mar 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.42→17.81 Å / Num. obs: 1864 / % possible obs: 87.5 % / Redundancy: 11.4 % / CC1/2: 1 / Net I/σ(I): 19.4
Reflection shellResolution: 2.421→2.924 Å / Redundancy: 8.1 % / Num. unique obs: 189 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal B type DNA duplexes generated in Cadnano

Resolution: 2.42→17.81 Å / SU ML: 0.2377 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2981 80 4.29 %
Rwork0.246 1784 -
obs0.2488 1864 41.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.11 Å2
Refinement stepCycle: LAST / Resolution: 2.42→17.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 325 0 0 325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112362
X-RAY DIFFRACTIONf_angle_d1.3363552
X-RAY DIFFRACTIONf_chiral_restr0.068163
X-RAY DIFFRACTIONf_plane_restr0.007516
X-RAY DIFFRACTIONf_dihedral_angle_d39.3191150
LS refinement shellResolution: 2.42→17.81 Å
RfactorNum. reflection% reflection
Rfree0.2981 80 -
Rwork0.246 1784 -
obs--41.5 %
Refinement TLS params.Method: refined / Origin x: 9.85558272544 Å / Origin y: 7.11623851631 Å / Origin z: 6.53292223312 Å
111213212223313233
T0.470149825604 Å20.151905105543 Å20.0455103913211 Å2-0.17683123066 Å20.0181150870426 Å2--0.299086250046 Å2
L1.32906659906 °20.078287484366 °2-0.392093643306 °2-1.52910554879 °20.69733951927 °2--1.61751283869 °2
S-0.257656854393 Å °-0.125145925663 Å °0.383851500124 Å °0.0783114368292 Å °0.735950444902 Å °0.0747689103829 Å °0.0691523244812 Å °0.501205004645 Å °1.55343920841 Å °
Refinement TLS groupSelection details: all

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