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- PDB-8f42: Engineering Crystals with Tunable Symmetries from 14- or 16-Base-... -

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Basic information

Entry
Database: PDB / ID: 8f42
TitleEngineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands
ComponentsDNA (5'-D(*CP*GP*CP*TP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*GP*C)-3')
KeywordsDNA / Four-Fold Rotational Axis / Left-Handed / Parallel
Function / homologyChem-HT1 / DNA / DNA (> 10)
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
DepositionNov 10, 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*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*GP*C)-3')
B: DNA (5'-D(*CP*GP*CP*TP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2493
Polymers9,7962
Non-polymers4531
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-0 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.363, 35.363, 103.291
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(*CP*GP*CP*TP*TP*AP*AP*GP*GP*AP*AP*TP*TP*CP*GP*C)-3')


Mass: 4898.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-HT1 / 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33342


Mass: 452.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N6O / Feature type: SUBJECT OF INVESTIGATION
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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 30 uM motif 60 uM Hoechst 33342, 0.005 M magnesium sulfate hydrate, 0.005 M HEPES sodium pH 7.0, 0.16 M lithium sulfate monohydrate, 6 % 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: Nov 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.55→35.363 Å / Num. obs: 4231 / % possible obs: 80 % / Redundancy: 6.5 % / CC1/2: 1 / Net I/σ(I): 12.7
Reflection shellResolution: 2.55→2.93 Å / Num. unique obs: 396 / CC1/2: 0.743

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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→35.36 Å / SU ML: 0.3376 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1347
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 187 4.42 %
Rwork0.2252 4044 -
obs0.2277 4231 51.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.37 Å2
Refinement stepCycle: LAST / Resolution: 2.55→35.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 650 34 0 684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122767
X-RAY DIFFRACTIONf_angle_d1.65111176
X-RAY DIFFRACTIONf_chiral_restr0.0631126
X-RAY DIFFRACTIONf_plane_restr0.00635
X-RAY DIFFRACTIONf_dihedral_angle_d39.3225329
LS refinement shellResolution: 2.55→35.36 Å
RfactorNum. reflection% reflection
Rfree0.2788 187 -
Rwork0.2252 4044 -
obs--51.88 %
Refinement TLS params.Method: refined / Origin x: 8.55046629729 Å / Origin y: -8.64607123775 Å / Origin z: -12.8374923827 Å
111213212223313233
T-0.0184841327584 Å2-0.612341801837 Å20.0513430877473 Å2-0.104247895887 Å20.100881345416 Å2--0.211725862812 Å2
L0.603071790781 °20.318140802066 °2-0.123676254949 °2-0.463176461617 °2-0.162357005601 °2--1.57336002522 °2
S0.9138147985 Å °0.278440490611 Å °-0.0199350491393 Å °0.216539895066 Å °0.85812018932 Å °-0.00761071317929 Å °-0.0391625181942 Å °-0.10358040677 Å °0.919072890122 Å °
Refinement TLS groupSelection details: all

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