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

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Entry
Database: PDB / ID: 8epf
TitleEngineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands
Components
  • DNA (5'-D(*AP*CP*GP*CP*TP*GP*GP*TP*GP*GP*TP*TP*CP*GP*CP*A)-3')
  • DNA (5'-D(*GP*TP*AP*CP*CP*AP*GP*CP*CP*GP*AP*AP*CP*CP*TP*G)-3')
KeywordsDNA / Four-Fold Rotational Axis / Left-Handed / Parallel
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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
A: DNA (5'-D(*GP*TP*AP*CP*CP*AP*GP*CP*CP*GP*AP*AP*CP*CP*TP*G)-3')
B: DNA (5'-D(*AP*CP*GP*CP*TP*GP*GP*TP*GP*GP*TP*TP*CP*GP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)9,7982
Polymers9,7982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-10 kcal/mol
Surface area6320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.582, 33.582, 105.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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


Mass: 4868.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*CP*GP*CP*TP*GP*GP*TP*GP*GP*TP*TP*CP*GP*CP*A)-3')


Mass: 4930.189 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: 3.05 Å3/Da / Density % sol: 59.66 %
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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.608→33.582 Å / Num. obs: 3756 / % possible obs: 80.5 % / Redundancy: 12.7 % / CC1/2: 1 / Net I/σ(I): 8.6
Reflection shellResolution: 2.608→3.06 Å / Redundancy: 14.1 % / Num. unique obs: 418 / CC1/2: 0.6

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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: 2.61→33.58 Å / SU ML: 0.6682 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2965 182 5.3 %
Rwork0.2141 3249 -
obs0.2198 3431 48.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.87 Å2
Refinement stepCycle: LAST / Resolution: 2.61→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 650 0 0 650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116728
X-RAY DIFFRACTIONf_angle_d1.31851120
X-RAY DIFFRACTIONf_chiral_restr0.0623126
X-RAY DIFFRACTIONf_plane_restr0.007932
X-RAY DIFFRACTIONf_dihedral_angle_d38.5774312
LS refinement shellResolution: 2.61→33.58 Å
RfactorNum. reflection% reflection
Rfree0.2965 182 -
Rwork0.2141 3249 -
obs--48.64 %

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