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

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Basic information

Entry
Database: PDB / ID: 8epb
TitleEngineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands
Components
  • DNA (5'-D(*CP*GP*CP*TP*GP*GP*TP*GP*GP*TP*TP*CP*GP*A)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*GP*CP*CP*GP*AP*AP*CP*CP*T)-3')
KeywordsDNA / Three-Fold Rotational Axis / Left-Handed / Parallel
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / 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(*CP*GP*CP*TP*GP*GP*TP*GP*GP*TP*TP*CP*GP*A)-3')
B: DNA (5'-D(*GP*AP*CP*CP*AP*GP*CP*CP*GP*AP*AP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)8,5632
Polymers8,5632
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-9 kcal/mol
Surface area5350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.970, 37.970, 69.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

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


Mass: 4327.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*AP*CP*CP*AP*GP*CP*CP*GP*AP*AP*CP*CP*T)-3')


Mass: 4234.771 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.5 ug/uL motif 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium, 0.16 M lithium sulfate monohydrate, 3 % 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 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.61→32.883 Å / Num. obs: 1876 / % possible obs: 80 % / Redundancy: 7.5 % / Biso Wilson estimate: 57.95 Å2 / CC1/2: 1 / Net I/σ(I): 17.3
Reflection shellResolution: 2.61→2.948 Å / Num. unique obs: 208 / CC1/2: 0.59

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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→29.73 Å / SU ML: 0.4979 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.0368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2926 86 4.6 %
Rwork0.2156 1785 -
obs0.2197 1871 54.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.58 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 568 0 0 568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133636
X-RAY DIFFRACTIONf_angle_d1.7152978
X-RAY DIFFRACTIONf_chiral_restr0.087110
X-RAY DIFFRACTIONf_plane_restr0.007928
X-RAY DIFFRACTIONf_dihedral_angle_d40.8527272
LS refinement shellResolution: 2.61→29.73 Å
RfactorNum. reflection% reflection
Rfree0.2926 86 -
Rwork0.2156 1785 -
obs--54.8 %
Refinement TLS params.Method: refined / Origin x: 8.67001770793 Å / Origin y: -5.50272986794 Å / Origin z: -4.96260107349 Å
111213212223313233
T0.219442423316 Å20.0443882950354 Å20.00778376603642 Å2-0.198900169464 Å20.0202622902702 Å2--0.236058518584 Å2
L0.417346648231 °2-0.121187466106 °20.0293694104019 °2-2.17778226387 °2-0.941299564924 °2--1.59660447113 °2
S0.141110905495 Å °-0.164728101181 Å °-0.0581565993096 Å °0.244240032914 Å °0.184165480694 Å °0.17917738694 Å °-0.205028015104 Å °-0.0184164409009 Å °0.00364514597889 Å °
Refinement TLS groupSelection details: all

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