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- PDB-9m6e: Crystal structure of xanthine/guanine RNA aptamer (P1-12bp) with ... -

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Basic information

Entry
Database: PDB / ID: 9m6e
TitleCrystal structure of xanthine/guanine RNA aptamer (P1-12bp) with hypoxanthine
ComponentsRNA (42-MER)
KeywordsRNA / xanthine/guanine RNA aptamer / hypoxanthine
Function / homologyGUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / HYPOXANTHINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLi, M. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: To Be Published
Title: Crystal structure of xanthine/guanine RNA aptamer
Authors: Li, M. / Huang, L.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 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: RNA (42-MER)
A: RNA (42-MER)
D: RNA (42-MER)
C: RNA (42-MER)
E: RNA (42-MER)
F: RNA (42-MER)
G: RNA (42-MER)
H: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,74525
Polymers107,7688
Non-polymers4,97717
Water00
1
F: RNA (42-MER)
hetero molecules

B: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1816
Polymers26,9422
Non-polymers1,2394
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
2
A: RNA (42-MER)
E: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2047
Polymers26,9422
Non-polymers1,2625
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: RNA (42-MER)
hetero molecules

H: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1816
Polymers26,9422
Non-polymers1,2394
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_546x,y-1,z+11
4
C: RNA (42-MER)
hetero molecules

G: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1816
Polymers26,9422
Non-polymers1,2394
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)22.766, 44.905, 209.564
Angle α, β, γ (deg.)89.910, 89.900, 89.950
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid -4 through -3 or (resid -2...
d_2ens_1(chain "B" and ((resid -4 and (name C1" or name...
d_3ens_1(chain "C" and (resid -4 through -3 or (resid -2...
d_4ens_1(chain "D" and ((resid -4 and (name C1" or name...
d_5ens_1(chain "E" and ((resid -4 and (name C1" or name...
d_6ens_1(chain "F" and (resid -4 through -3 or (resid -2...
d_7ens_1(chain "G" and ((resid -4 and (name C1" or name...
d_8ens_1(chain "H" and (resid -4 through -3 or (resid -2...

NCS oper:
IDCodeMatrixVector
1given(-0.9989577784, 0.0351469348643, 0.0291212970947), (-0.0383497445223, -0.992281776379, -0.117924439202), (0.024751849828, -0.118918330108, 0.992595474851)-2.39511295929, 22.9594325627, -8.15107183959
2given(-0.999997240188, -0.00203153869511, 0.00118002843152), (0.00203437354234, -0.999995035887, 0.0024061433259), (0.00117513440045, 0.00240853730402, 0.999996408997)-12.5238816656, 1.18736022949, 104.80631686
3given(0.999040190794, -0.0354246871801, -0.0257640974469), (0.0383156124279, 0.991780154952, 0.122082095687), (0.0212276005081, -0.12295208734, 0.992185553813)-10.1797573036, -21.9197561054, 96.635944038
4given(0.998728083158, -0.0397796751521, -0.0309805318998), (-0.0432334109317, -0.99180430573, -0.120229328011), (-0.02594394132, 0.12141580037, -0.992262624172)1.27324115204, 0.69633964386, 112.244324397
5given(-0.999991868436, -0.00357550340206, -0.00186516404963), (-0.00356932350201, 0.999988164414, -0.00330620036007), (0.00187696330496, -0.00329951610161, -0.999992795075)-1.18238378918, -22.288907568, 104.087724056
6given(-0.99882335313, 0.0401758339735, 0.0271626877636), (0.0431280167828, 0.991998920937, 0.11865123273), (-0.0221784447243, 0.119683094982, -0.992564392554)-13.7624870228, 0.40019586535, 7.47576769998
7given(0.999999117448, 0.00105538006387, -0.000807017012208), (0.00105676032479, -0.999997976471, 0.00171181505645), (-0.000805208763702, -0.00171266636924, -0.999998209205)-11.3988607097, 23.3407710154, -0.713795261766

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Components

#1: RNA chain
RNA (42-MER)


Mass: 13470.997 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H4N4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: 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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.08 M Potassium chloride 0.02 M Magnesium chloride hexahydrate 48% 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: 0.97895 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.95→104.78 Å / Num. obs: 17227 / % possible obs: 98.4 % / Redundancy: 3 % / Biso Wilson estimate: 46.73 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.156 / Net I/σ(I): 4.1
Reflection shellResolution: 2.95→3.11 Å / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2447 / CC1/2: 0.914 / Rpim(I) all: 0.646 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→34.93 Å / SU ML: 0.5108 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.3365
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2715 893 5.27 %
Rwork0.246 16059 -
obs0.2474 16952 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.03 Å2
Refinement stepCycle: LAST / Resolution: 2.95→34.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6960 321 0 7281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028104
X-RAY DIFFRACTIONf_angle_d0.644512596
X-RAY DIFFRACTIONf_chiral_restr0.02851672
X-RAY DIFFRACTIONf_plane_restr0.0027344
X-RAY DIFFRACTIONf_dihedral_angle_d16.32774016
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2KAX-RAY DIFFRACTIONTorsion NCS0.770922117991
ens_1d_3KAX-RAY DIFFRACTIONTorsion NCS0.157448088548
ens_1d_4KAX-RAY DIFFRACTIONTorsion NCS0.763757915077
ens_1d_5KAX-RAY DIFFRACTIONTorsion NCS0.770458984907
ens_1d_6KAX-RAY DIFFRACTIONTorsion NCS0.176617090692
ens_1d_7KAX-RAY DIFFRACTIONTorsion NCS0.772783850654
ens_1d_8KAX-RAY DIFFRACTIONTorsion NCS0.159425168953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.130.42981360.35612584X-RAY DIFFRACTION92.9
3.13-3.380.29541360.31472662X-RAY DIFFRACTION95.72
3.38-3.720.32591580.2852689X-RAY DIFFRACTION97.23
3.72-4.250.2811480.23562689X-RAY DIFFRACTION98.34
4.25-5.350.20971460.20722728X-RAY DIFFRACTION99
5.36-34.930.21791690.19112707X-RAY DIFFRACTION98.39

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