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- PDB-9u3i: Crystal structure of a phenylalanine-modifi ed thrombin-binding D... -

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Basic information

Entry
Database: PDB / ID: 9u3i
TitleCrystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer
ComponentsDNA (5'-D(*GP*G*(FNH)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / aptamer
Function / homology: / PHENYLALANINE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPark, S. / Kanazawa, H. / Kondo, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Crystal structure of a phenylalanine-modifi ed thrombin-binding DNA aptamer
Authors: Park, S. / Kanazawa, H. / Kondo, J.
History
DepositionMar 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*GP*G*(FNH)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9083
Polymers4,6061
Non-polymers3032
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.055, 54.440, 21.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-243-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*G*(FNH)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')


Mass: 4605.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2 / Source: (synth.) DNA molecule (others) / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: MOPS, spermine, barium 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: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→27.62 Å / Num. obs: 12268 / % possible obs: 99.3 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.082 / Net I/σ(I): 22.73
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.2-1.230.3238670.9920.3361
1.23-1.260.278680.9920.2811
1.26-1.30.2688280.9950.2791
1.3-1.340.2448240.9950.2551
1.34-1.380.2337870.9930.2431
1.38-1.430.1897820.9950.1971
1.43-1.490.1637190.9960.171
1.49-1.550.1417340.9980.1471
1.55-1.620.1086890.9970.1131
1.62-1.690.0956670.9970.11
1.69-1.790.0876460.9980.0911
1.79-1.890.0825960.9960.0861
1.89-2.030.0815740.9960.0851
2.03-2.190.0735310.9980.0761
2.19-2.40.0735040.9970.0761
2.4-2.680.0654550.9980.0681
2.68-3.090.0653970.9980.0681
3.09-3.790.0563500.9990.0591
3.79-5.360.052880.9990.0521
5.36-27.620.0491620.9980.0521

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D31

7d31


Resolution: 1.2→27.62 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 1228 10.01 %
Rwork0.1787 --
obs0.1814 12263 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 305 12 67 384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019351
X-RAY DIFFRACTIONf_angle_d1.346536
X-RAY DIFFRACTIONf_dihedral_angle_d33.308135
X-RAY DIFFRACTIONf_chiral_restr0.04458
X-RAY DIFFRACTIONf_plane_restr0.05117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.250.1991310.18471180X-RAY DIFFRACTION97
1.25-1.30.18751320.17571188X-RAY DIFFRACTION99
1.3-1.370.22981330.17641191X-RAY DIFFRACTION99
1.37-1.460.19791330.18011205X-RAY DIFFRACTION99
1.46-1.570.19031360.1741211X-RAY DIFFRACTION99
1.57-1.730.18811360.17051230X-RAY DIFFRACTION100
1.73-1.980.19491380.17521240X-RAY DIFFRACTION100
1.98-2.490.20781400.19011254X-RAY DIFFRACTION100
2.49-27.620.2171490.17721336X-RAY DIFFRACTION99

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