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- PDB-9ehb: Structure of short Lettuce aptamer (C14T variant) bound with TO1-... -

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Basic information

Entry
Database: PDB / ID: 9ehb
TitleStructure of short Lettuce aptamer (C14T variant) bound with TO1-biotin.
ComponentsDNA 53-mer
KeywordsDNA / Structure of short Lettuce aptamer (C14T variant) bound with TO1-biotin.
Function / homologyDIMETHYLFORMAMIDE / Chem-HZD / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKoomullam, N. / Batchelder-Schwab, E. / Mao, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CCF 2107393 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: DNA 53-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4947
Polymers16,5581
Non-polymers9366
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.179, 44.690, 120.288
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 DNA 53-mer


Mass: 16557.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 uM annealed DNA (in 20 mM MOPS KOH pH 7.0, 150 mM KCl, 1 mM MgCl2 and 10 uM EDTA) was mixed with equimolar chromophore and mixed with crystallization buffer solution (1 M magnesium ...Details: 100 uM annealed DNA (in 20 mM MOPS KOH pH 7.0, 150 mM KCl, 1 mM MgCl2 and 10 uM EDTA) was mixed with equimolar chromophore and mixed with crystallization buffer solution (1 M magnesium chloride hexahydrate, 2 M HEPES pH 7.5 and PEG MME 550) and crystallized against 300 uL crystallization buffer and 300 uL water mixture.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.03→30.07 Å / Num. obs: 9274 / % possible obs: 99.4 % / Redundancy: 5.9 % / Biso Wilson estimate: 46.27 Å2 / CC1/2: 0.997 / Net I/σ(I): 5.6
Reflection shellResolution: 2.03→2.06 Å / Num. unique obs: 462 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→30.07 Å / SU ML: 0.405 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2821 414 5.03 %
Rwork0.2327 7819 -
obs0.2352 8233 88.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.77 Å2
Refinement stepCycle: LAST / Resolution: 2.03→30.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1100 42 38 1180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961276
X-RAY DIFFRACTIONf_angle_d1.20991963
X-RAY DIFFRACTIONf_chiral_restr0.0582211
X-RAY DIFFRACTIONf_plane_restr0.009157
X-RAY DIFFRACTIONf_dihedral_angle_d33.8805536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.330.41591420.35662618X-RAY DIFFRACTION90.82
2.33-2.930.36681430.33962637X-RAY DIFFRACTION90.94
2.93-30.070.23721290.18492564X-RAY DIFFRACTION83.3
Refinement TLS params.Method: refined / Origin x: -5.77783297248 Å / Origin y: 3.73440299572 Å / Origin z: -16.5231675352 Å
111213212223313233
T0.318964938948 Å20.122731944114 Å20.00984720483247 Å2-0.559171845517 Å20.029104884275 Å2--0.285696098589 Å2
L2.05735011126 °2-0.450464422476 °21.72979976508 °2-2.91861730027 °2-1.82403300607 °2--6.19537993979 °2
S-0.111545417246 Å °-0.620941336431 Å °-0.181673532495 Å °0.384604829578 Å °0.495213659774 Å °0.0724021751177 Å °-0.0570448488221 Å °-0.566064736454 Å °-0.326710392289 Å °
Refinement TLS groupSelection details: all

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