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- PDB-8k0w: Crystal structure of theophylline DNA aptamer bound to theophylli... -

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Basic information

Entry
Database: PDB / ID: 8k0w
TitleCrystal structure of theophylline DNA aptamer bound to theophylline, soaked in Selenourea
ComponentsDNA (29-MER)
KeywordsDNA / Aptamer / Theophylline
Function / homologyTHEOPHYLLINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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)9,2388
Polymers8,9191
Non-polymers3197
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area4980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.117, 50.117, 50.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

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Components

#1: DNA chain DNA (29-MER)


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


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Calcium chloride dihydrate 24% v/v Polyethylene glycol 400 40mM Barium Chloride

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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: 1.42→43.4 Å / Num. obs: 14214 / % possible obs: 100 % / Redundancy: 37.1 % / Biso Wilson estimate: 18.7 Å2 / CC1/2: 1 / Net I/σ(I): 24.8
Reflection shellResolution: 1.42→1.5 Å / Num. unique obs: 2034 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→25.06 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.0315
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 712 5.04 %
Rwork0.2081 13420 -
obs0.2088 14132 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.67 Å2
Refinement stepCycle: LAST / Resolution: 1.42→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 591 19 83 693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145675
X-RAY DIFFRACTIONf_angle_d1.72111040
X-RAY DIFFRACTIONf_chiral_restr0.0783115
X-RAY DIFFRACTIONf_plane_restr0.018230
X-RAY DIFFRACTIONf_dihedral_angle_d32.4649286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.530.29251390.272620X-RAY DIFFRACTION99.57
1.53-1.690.25831360.22982660X-RAY DIFFRACTION99.33
1.69-1.930.25931390.25232666X-RAY DIFFRACTION99.43
1.93-2.440.27761470.25742678X-RAY DIFFRACTION99.93
2.44-25.060.18541510.17412796X-RAY DIFFRACTION99.59
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)
11.995584401351.03518971068-0.7416289682852.58431790925-2.154120319355.49879173796-0.07757076800990.4510802140160.230179068085-0.2763545621610.1806704715080.0890881433475-0.3839532009170.0311055951457-0.08191842044270.219861237093-0.04775128397170.01303458159290.259587296820.05081045038070.20681647270813.8329410175-9.2431269818-2.88494094608
22.2288898847-0.991371788921-0.477188377994.89514861223.904509380713.20918850563-0.0424078432143-0.0716166360366-0.07894062932990.43132240936-0.0002252643483980.2059222320290.505617226305-0.03550437144150.1118939034820.193762699941-0.01308309767720.0055504424660.1892535500060.02526328543770.14564866804816.447627262-18.947723897313.2137432319
32.420776326190.704849876685-0.5904865781012.97547782602-0.7936711335752.759709584590.1888988478940.331813560820.212141431452-0.1285465604730.06976866194220.349713679196-0.324389329407-0.131482798194-0.2292600044590.1874481389260.02039686707660.003597133528280.2110869127840.03440841700830.16325252713414.8970962614-9.7815046573-1.43333246355
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 29 )AA16 - 29

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