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- PDB-9ja9: Crystal structure of theophylline aptamer -

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Basic information

Entry
Database: PDB / ID: 9ja9
TitleCrystal structure of theophylline aptamer
ComponentsTheophylline aptamer
KeywordsRNA / theophylline aptamer / caffeine
Function / homology: / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsKondo, J. / Ohtani, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121014 Japan
CitationJournal: To Be Published
Title: Crystal structure of theophylline aptamer
Authors: Kondo, J. / Ohtani, Y.
History
DepositionAug 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Theophylline aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6438
Polymers10,6371
Non-polymers1,0067
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-3 kcal/mol
Surface area5850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.853, 46.853, 180.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain Theophylline aptamer


Mass: 10637.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: MOPS (pH7), Hexammine cobalt chloride, Potassium chloride, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.605 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.605 Å / Relative weight: 1
ReflectionResolution: 2.68→33.64 Å / Num. obs: 6222 / % possible obs: 99.7 % / Redundancy: 5.05 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.069 / Net I/σ(I): 14.41
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.68-2.750.3994730.9970.4521
2.75-2.830.2384250.9880.2641
2.83-2.910.1874630.9940.211
2.91-30.1174080.9950.1311
3-3.10.0841910.0891
3.1-3.20.0663810.9990.0721
3.2-3.320.0643900.9980.071
3.32-3.460.0593640.9990.0641
3.46-3.610.0673640.9980.0721
3.61-3.790.0583290.9990.0621
3.79-40.0533300.9990.0581
4-4.240.0623070.9980.0671
4.24-4.530.0572770.9980.0631
4.53-4.890.0542640.9970.061
4.89-5.360.0562530.9970.0631
5.36-5.990.0532180.9970.061
5.99-6.920.051950.9940.0571
6.92-8.480.0491660.9930.0561
8.48-11.990.0411320.9970.0461
11.99-33.640.035640.9980.041

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→33.64 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 623 10.15 %
Rwork0.1892 --
obs0.19 6137 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 704 43 5 752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.967
X-RAY DIFFRACTIONf_dihedral_angle_d12.048392
X-RAY DIFFRACTIONf_chiral_restr0.04164
X-RAY DIFFRACTIONf_plane_restr0.00733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.950.35041570.2921382X-RAY DIFFRACTION98
2.95-3.370.23871530.25311346X-RAY DIFFRACTION96
3.38-4.250.22041570.1751397X-RAY DIFFRACTION99
4.25-33.640.14531560.15381389X-RAY DIFFRACTION100

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