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

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Basic information

Entry
Database: PDB / ID: 8epi
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*GP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*TP*A)-3')
KeywordsDNA / Four-Fold Rotational Axis / Left-Handed / Parallel
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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*GP*GP*A)-3')
A: DNA (5'-D(*CP*GP*AP*CP*G)-3')
B: DNA (5'-D(P*TP*CP*CP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)4,8093
Polymers4,8093
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-5 kcal/mol
Surface area3600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.377, 36.377, 104.372
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*GP*GP*A)-3')


Mass: 1849.241 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*TP*CP*CP*TP*A)-3')


Mass: 1454.999 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: 3.59 Å3/Da / Density % sol: 65.74 %
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-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.55→36.38 Å / Num. obs: 1308 / % possible obs: 80.4 % / Redundancy: 10.8 % / CC1/2: 1 / Net I/σ(I): 12.2
Reflection shellResolution: 2.555→3.117 Å / Redundancy: 10.1 % / Num. unique obs: 188 / CC1/2: 0.9

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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: 2.55→36.38 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 28.7215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2911 63 4.82 %
Rwork0.249 1243 -
obs0.2511 1306 50.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.76 Å2
Refinement stepCycle: LAST / Resolution: 2.55→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 325 0 0 325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119362
X-RAY DIFFRACTIONf_angle_d1.5552
X-RAY DIFFRACTIONf_chiral_restr0.075563
X-RAY DIFFRACTIONf_plane_restr0.007816
X-RAY DIFFRACTIONf_dihedral_angle_d39.7039150
LS refinement shellResolution: 2.55→36.38 Å
RfactorNum. reflection% reflection
Rfree0.2911 63 -
Rwork0.249 1243 -
obs--50.42 %
Refinement TLS params.Method: refined / Origin x: 9.52536341184 Å / Origin y: 6.25966734034 Å / Origin z: 6.61675723803 Å
111213212223313233
T0.546977341365 Å20.130135277708 Å20.151439969507 Å2-0.0880806858036 Å20.0526627509056 Å2--0.371610785957 Å2
L1.34448652125 °2-0.80171128952 °2-0.593411741289 °2-1.31087378945 °20.251480022352 °2--1.80956856072 °2
S0.437222729242 Å °-0.361439331701 Å °0.283254015575 Å °-0.0768279751361 Å °0.827117343347 Å °-0.0734260249667 Å °-0.0311503134483 Å °0.292109505102 Å °1.02987548256 Å °
Refinement TLS groupSelection details: all

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