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- PDB-9ehe: Structure of short Lettuce aptamer (A5T variant) bound with TO1-b... -

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Basic information

Entry
Database: PDB / ID: 9ehe
TitleStructure of short Lettuce aptamer (A5T variant) bound with TO1-biotin.
ComponentsDNA 53-mer
KeywordsDNA / Structure of short Lettuce aptamer (A5T 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: 1.63 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)17,4456
Polymers16,5341
Non-polymers9125
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.456, 43.258, 118.383
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: 16533.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 77 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.: 2 / 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.: 72 / 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: 1.89 Å3/Da / Density % sol: 35.05 %
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: 1.63→29.6 Å / Num. obs: 16644 / % possible obs: 87.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 1.63→1.84 Å / Num. unique obs: 464 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→29.6 Å / SU ML: 0.2879 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.85
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 883 5.31 %
Rwork0.2231 15761 -
obs0.2256 16644 54.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.01 Å2
Refinement stepCycle: LAST / Resolution: 1.63→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1098 42 72 1212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971274
X-RAY DIFFRACTIONf_angle_d1.20151959
X-RAY DIFFRACTIONf_chiral_restr0.0556211
X-RAY DIFFRACTIONf_plane_restr0.009157
X-RAY DIFFRACTIONf_dihedral_angle_d34.2781537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.730.3178200.3275319X-RAY DIFFRACTION6.68
1.73-1.860.3823360.2844512X-RAY DIFFRACTION10.92
1.86-2.050.271600.35721192X-RAY DIFFRACTION24.69
2.05-2.350.36162190.33124187X-RAY DIFFRACTION87.61
2.35-2.950.3413150.29154761X-RAY DIFFRACTION99.96
2.96-29.60.21462330.16654790X-RAY DIFFRACTION98.94
Refinement TLS params.Method: refined / Origin x: -5.38250133064 Å / Origin y: -4.39172045297 Å / Origin z: 16.3182794046 Å
111213212223313233
T0.144549366013 Å2-0.0158775554312 Å20.0596163125802 Å2-0.209338514066 Å20.0506648505531 Å2--0.200857869899 Å2
L0.625036745951 °20.732230135006 °2-1.26045577462 °2-3.44356344431 °2-2.4166551055 °2--9.18748228077 °2
S0.0246468103554 Å °0.0537667758275 Å °0.229036909965 Å °-0.313584062509 Å °-0.0245612420832 Å °-0.266900422962 Å °-0.186752678842 Å °0.301637947676 Å °-0.0304330156467 Å °
Refinement TLS groupSelection details: all

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