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- PDB-9ja7: Crystal structure of theophylline aptamer obtained in the presenc... -

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Basic information

Entry
Database: PDB / ID: 9ja7
TitleCrystal structure of theophylline aptamer obtained in the presence of caffeine
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 / SAD / Resolution: 2.59 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 obtained in the presence of caffeine
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

Downloads & links

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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
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-3 kcal/mol
Surface area5860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.925, 46.925, 180.258
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.: 1 / 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: 54.32 %
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: 2.59→33.66 Å / Num. obs: 6866 / % possible obs: 99.7 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.059 / Net I/σ(I): 16.42
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.59-2.660.3374850.9510.3771
2.66-2.730.2735060.9810.3051
2.73-2.810.2114850.9930.2361
2.81-2.90.134650.9980.1451
2.9-2.990.0924540.9970.1041
2.99-3.10.0634500.9990.071
3.1-3.220.0524090.9990.0581
3.22-3.350.0534250.9990.0581
3.35-3.50.0513710.9990.0561
3.5-3.670.0563820.9990.0621
3.67-3.870.0443630.9990.0481
3.87-4.10.0493280.9980.0541
4.1-4.380.0493180.9980.0541
4.38-4.730.0513020.9950.0571
4.73-5.190.0512730.9970.0561
5.19-5.80.0512420.9970.0571
5.8-6.70.0442170.9970.0491
6.7-8.20.0511780.9940.0571
8.2-11.60.0451430.9980.051
11.6-33.660.037700.9970.0421

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XSCALEdata scaling
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→33.66 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 34.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2603 677 9.98 %
Rwork0.206 --
obs0.2114 6785 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 704 43 1 748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d1.013
X-RAY DIFFRACTIONf_dihedral_angle_d11.738392
X-RAY DIFFRACTIONf_chiral_restr0.045164
X-RAY DIFFRACTIONf_plane_restr0.00733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.790.44651330.36541217X-RAY DIFFRACTION98
2.79-3.070.35781310.31021215X-RAY DIFFRACTION98
3.07-3.520.28931430.25291191X-RAY DIFFRACTION97
3.52-4.430.2461300.1881244X-RAY DIFFRACTION100
4.43-33.660.2081400.15271241X-RAY DIFFRACTION100

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