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- PDB-9ehc: Structure of short Lettuce aptamer bound to TO1-3PEG-Biotin -

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Basic information

Entry
Database: PDB / ID: 9ehc
TitleStructure of short Lettuce aptamer bound to TO1-3PEG-Biotin
Components53-mer DNA
KeywordsDNA / Aptamer / Chromophore
Function / homologyDIMETHYLFORMAMIDE / Chem-HZD / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBatchelder-schwab, E. / Koomullam kattil, N. / Mao, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CCF2107393 United States
CitationJournal: ACS Sens / Year: 2026
Title: Fluorogenic Aptamer Optimization on a Massively Parallel Sequencing Platform.
Authors: Kuo, Y.A. / Chen, Y.I. / Siraj, N. / He, Y. / Yang, Z. / Wang, Y. / Batchelder-Schwab, E.J. / Korkmaz, Z. / Yonas, S. / Nguyen, T.D. / Hong, S. / Nguyen, A.T. / Kim, S. / Seifi, S. / Fan, P. ...Authors: Kuo, Y.A. / Chen, Y.I. / Siraj, N. / He, Y. / Yang, Z. / Wang, Y. / Batchelder-Schwab, E.J. / Korkmaz, Z. / Yonas, S. / Nguyen, T.D. / Hong, S. / Nguyen, A.T. / Kim, S. / Seifi, S. / Fan, P.H. / Wu, Y. / Liu, H.W. / Lu, Y. / Ren, P. / Mao, C. / Yeh, H.C.
History
DepositionNov 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 53-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5508
Polymers16,5431
Non-polymers1,0087
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.362, 43.489, 119.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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DNA chain , 1 types, 1 molecules B

#1: DNA chain 53-mer DNA


Mass: 16542.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 61 molecules

#2: Chemical ChemComp-HZD / 4-[(3-{2,16-dioxo-20-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium


Mass: 750.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: MOPS KOH pH 7.0, KCl, MgCl2, EDTA, as annealing buffer. MgCl2, HEPES, PEG MME 550 chamber buffer and drop crystallization buffer.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2024
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→40.86 Å / Num. obs: 13533 / % possible obs: 89.4 % / Observed criterion σ(I): 1.2 / Redundancy: 6.2 % / Biso Wilson estimate: 18.06 Å2 / CC1/2: 0.98 / Net I/σ(I): 7.1
Reflection shellResolution: 1.5→1.68 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3708 / CC1/2: 0.609 / % possible all: 49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.83 Å / SU ML: 0.1784 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.6726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2838 642 4.76 %
Rwork0.2375 12856 -
obs0.2396 13498 64.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.72 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1099 48 54 1201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01391280
X-RAY DIFFRACTIONf_angle_d1.6311966
X-RAY DIFFRACTIONf_chiral_restr0.0813211
X-RAY DIFFRACTIONf_plane_restr0.014458
X-RAY DIFFRACTIONf_dihedral_angle_d34.9822538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.620.4173150.3556330X-RAY DIFFRACTION8.34
1.62-1.780.3032780.28021299X-RAY DIFFRACTION33.57
1.78-2.040.32141680.29743052X-RAY DIFFRACTION77.14
2.04-2.570.33341700.29863978X-RAY DIFFRACTION98.81
2.57-29.830.25612110.20074197X-RAY DIFFRACTION99.39
Refinement TLS params.Method: refined / Origin x: -5.52176303845 Å / Origin y: 4.1202924089 Å / Origin z: -16.331850927 Å
111213212223313233
T0.0886837808765 Å2-0.0366962342121 Å2-0.063503704818 Å2-0.094765920605 Å20.056401018265 Å2--0.138860640305 Å2
L1.13437121567 °2-1.00681668283 °20.881519584248 °2-3.50359317134 °2-1.87880888212 °2--6.89651565985 °2
S0.0414683454984 Å °-0.0073938099915 Å °-0.158491515908 Å °0.38780866863 Å °-0.0851309140891 Å °-0.282669665829 Å °0.0351305507175 Å °0.230710612559 Å °0.00571581874236 Å °
Refinement TLS groupSelection details: all

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