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- PDB-8k0t: Crystal structure of theophylline DNA aptamer bound to theophylline -

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Basic information

Entry
Database: PDB / ID: 8k0t
TitleCrystal structure of theophylline DNA aptamer bound to theophylline
ComponentsDNA (29-MER)
KeywordsDNA / Aptamer / Theophylline
Function / homologyIODIDE ION / : / THEOPHYLLINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHuang, Y. / Lin, X. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: From Theophylline to Adenine or preQ 1 : Repurposing a DNA Aptamer Revealed by Crystal Structure Analysis.
Authors: Lin, X. / Huang, Y. / Huang, J. / Yuan, H. / Luo, Y. / Lu, Z. / Ao, Y. / Huang, J. / Chen, S.B. / Miao, Z. / Huang, L.
History
DepositionJul 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 18, 2025Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2885
Polymers8,9191
Non-polymers3694
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-8 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.747, 41.244, 34.157
Angle α, β, γ (deg.)90.000, 113.320, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-102-

K

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (29-MER)


Mass: 8918.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 9 molecules

#2: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M Calcium chloride dihydrate 32% v/v Polyethylene glycol 400 0.002M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.82→31.38 Å / Num. obs: 7284 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 52.01 Å2 / CC1/2: 1 / Net I/σ(I): 21.3
Reflection shellResolution: 1.82→1.87 Å / Num. unique obs: 537 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→31.37 Å / SU ML: 0.4565 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 38.4845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2893 277 5.1 %
Rwork0.2612 5150 -
obs0.2626 5427 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.92 Å2
Refinement stepCycle: LAST / Resolution: 2→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 591 16 5 612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129675
X-RAY DIFFRACTIONf_angle_d1.27671040
X-RAY DIFFRACTIONf_chiral_restr0.0619115
X-RAY DIFFRACTIONf_plane_restr0.010930
X-RAY DIFFRACTIONf_dihedral_angle_d33.6383286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.520.51821350.41412564X-RAY DIFFRACTION99.23
2.52-31.370.25091420.23822586X-RAY DIFFRACTION97.99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.518623163063.37842223304-0.7176453008973.35170520607-2.127582387616.022846088470.6696469999350.5136981047850.7097814571380.3213418465460.2606947593180.355597706166-0.2727993968260.24808086512-0.7455755367510.54415042102-0.06844747424450.04271824328410.573437173554-0.07031254089890.633353786721-8.9543125517-1.12817157921-10.0174145152
29.15980544625-0.108835430438-3.845720794868.643184678330.7470704781526.885491777360.7438839729960.1020631505481.814763867080.927110607455-0.508052148896-0.393471883530.214103883470.143647986739-0.3771890040410.629986756135-0.1108498154080.2675080649340.57268584666-0.1194358909640.817156577763-25.9833950036-5.42173612492-1.28653783883
34.82265632322-0.2953108566190.7387373470625.787157830221.264592950093.323542680350.151487090041-1.326661606770.1333329613681.20143644154-0.12509294250.06793894760431.159479060150.499311344799-0.02907947454760.763787849655-0.1756988164690.09500329639630.522316133465-0.228258880660.739894717931-14.7306665915-8.35128512101-3.37586238247
47.487034416733.90513868579-3.255396463074.32105706385-2.948634532145.252426697020.2704518930481.101138090251.257705311150.4523553310940.05653072531530.815931247435-0.527840704902-0.276512553015-0.3353164290780.509559962217-0.02768272052110.08560290367510.6008722243890.03623133579590.615029466266-7.783175761520.110326424129-11.6436350353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 15 )AA11 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 20 )AA16 - 20
4X-RAY DIFFRACTION4chain 'A' and (resid 21 through 29 )AA21 - 29

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