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- PDB-8zas: Crystal structure of Adenine DNA aptamer bound with adenine -

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Basic information

Entry
Database: PDB / ID: 8zas
TitleCrystal structure of Adenine DNA aptamer bound with adenine
Components
  • DNA (5'-D(*CP*AP*TP*TP*GP*GP*CP*GP*TP*CP*CP*GP*CP*CP*GP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*CP*GP*GP*TP*GP*GP*TP*CP*TP*AP*TP*T)-3')
KeywordsDNA / Aptamer / Adenine
Function / homologyADENINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsLin, 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
DepositionApr 25, 2024Deposition 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 25, 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 (5'-D(*GP*GP*GP*CP*GP*GP*TP*GP*GP*TP*CP*TP*AP*TP*T)-3')
B: DNA (5'-D(*CP*AP*TP*TP*GP*GP*CP*GP*TP*CP*CP*GP*CP*CP*GP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2604
Polymers10,1022
Non-polymers1582
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-24 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.366, 26.929, 63.532
Angle α, β, γ (deg.)90.000, 96.380, 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

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*CP*GP*GP*TP*GP*GP*TP*CP*TP*AP*TP*T)-3')


Mass: 4672.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*GP*GP*CP*GP*TP*CP*CP*GP*CP*CP*GP*CP*CP*C)-3')


Mass: 5429.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.08 M Sodium chloride, 0.02 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 6.0 35% v/v (+/-)-2-Methyl-2,4-pentanediol 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.54→31.57 Å / Num. obs: 3530 / % possible obs: 95.34 % / Redundancy: 6.7 % / Biso Wilson estimate: 88.28 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.061 / Net I/σ(I): 6
Reflection shellResolution: 2.54→2.631 Å / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 319 / CC1/2: 0.773 / Rpim(I) all: 0.045 / % possible all: 87.28

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8K0W

8k0w


Resolution: 2.54→31.57 Å / SU ML: 0.2811 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.3925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2751 181 5.32 %
Rwork0.218 3219 -
obs0.22 3397 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.29 Å2
Refinement stepCycle: LAST / Resolution: 2.54→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 669 11 0 680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049758
X-RAY DIFFRACTIONf_angle_d0.70781165
X-RAY DIFFRACTIONf_chiral_restr0.0334130
X-RAY DIFFRACTIONf_plane_restr0.003534
X-RAY DIFFRACTIONf_dihedral_angle_d34.6576322
LS refinement shellResolution: 2.54→2.67 Å
RfactorNum. reflection% reflection
Rfree0.2757 181 -
Rwork0.2172 3219 -
obs--95.05 %
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)
14.13727406793-0.475856679678-1.949196830870.651446019558-1.178808258661.968062281210.198314853069-0.7341394986550.9801368192880.3661609033460.340830454355-0.27012700621-0.639391581562-0.246549230655-0.4538408108041.017863003040.1331564612310.05140315710991.27405832641-0.1178167476570.94049463584413.115598586510.522408656616.2730033828
23.296705441582.375555049075.012912784673.897098516053.757044459947.6281104402-1.17999497440.19356170773.32841523792-1.34069174104-1.054672474243.41779959264-0.09364932017150.4038378721291.94411829231.11378648910.6664089354740.6231728687950.595700620940.7465509134062.288597980998.1135114968411.361891943821.5157103515
35.64737220192-2.09693597636-1.617084776735.692896370512.49589630611.57348388563-1.629320075230.739589550169-0.344625857610.1811205700911.08320696560.02742193517731.393892809240.1915152125890.5920964316371.00020594404-0.01382328386170.09398714340190.8798334342850.03441676478680.7159424810261.572140400634.9600267771124.5153276842
40.36604770484-0.899690721086-0.3230652918472.27607972795-0.2939544737471.44477467466-0.113387640616-0.4669412135920.30927453475-0.268158650205-0.16571573146-0.0690125303389-0.210325660668-0.3660277852450.1740131181211.159536324530.02044844387260.04204423573341.26326396883-0.0860265611131.115265299985.8638515058415.760836006914.8429432516
52.944704767550.27312413511-0.5998529452231.244688412030.216555414894.68164056851-0.397199876894-0.2649832480490.6604687004280.05468786699130.0633737523291-0.0876892089740.1127453199650.8318798916830.3350874037631.0567897081-0.007527018392360.06224949433521.19357766416-0.06132665196861.0538541020421.19892386447.003017222989.80019612652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 13 )AA-1 - 13
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 101 )AB101
3X-RAY DIFFRACTION3chain 'B' and (resid 14 through 18 )BC14 - 18
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 23 )BC19 - 23
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 31 )BC24 - 31

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