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- PDB-9m69: Crystal structure of xanthine/guanine RNA aptamer (P1 12bp) with ... -

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Basic information

Entry
Database: PDB / ID: 9m69
TitleCrystal structure of xanthine/guanine RNA aptamer (P1 12bp) with xanthine
ComponentsRNA (42-MER)
KeywordsRNA / xanthine/guanine RNA aptamer / xanthine
Function / homologyGUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / XANTHINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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
A: RNA (42-MER)
B: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2598
Polymers26,9422
Non-polymers1,3176
Water93752
1
A: RNA (42-MER)
hetero molecules

B: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2598
Polymers26,9422
Non-polymers1,3176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Unit cell
Length a, b, c (Å)23.006, 44.742, 210.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and ((resid -4 and (name C1" or name...
d_2ens_1(chain "B" and (resid -4 through -3 or (resid -2...

NCS oper: (Code: givenMatrix: (-0.997330003988, 0.0729609641217, 0.00309206383842), (-0.0728426648908, -0.990925655987, -0.112961455724), (-0.00517777133075, -0.112885083257, 0.993594559497)Vector: - ...NCS oper: (Code: given
Matrix: (-0.997330003988, 0.0729609641217, 0.00309206383842), (-0.0728426648908, -0.990925655987, -0.112961455724), (-0.00517777133075, -0.112885083257, 0.993594559497)
Vector: -0.828004610462, 35.9029744053, -7.31121714704)

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (42-MER)


Mass: 13470.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 58 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.08 M Potassium chloride 0.02 M Magnesium chloride hexahydrate 50% v/v (+/-)-2-Methy1-2,4-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: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.19→105.27 Å / Num. obs: 11672 / % possible obs: 95.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 47.34 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.073 / Net I/σ(I): 4.6
Reflection shellResolution: 2.19→2.3 Å / Rmerge(I) obs: 1.266 / Num. unique obs: 1401 / CC1/2: 0.476 / Rpim(I) all: 0.939 / % possible all: 80.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→34.09 Å / SU ML: 0.4482 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.7431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2959 565 4.97 %
Rwork0.2509 10794 -
obs0.2531 11359 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.28 Å2
Refinement stepCycle: LAST / Resolution: 2.19→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1740 84 52 1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012028
X-RAY DIFFRACTIONf_angle_d1.46273153
X-RAY DIFFRACTIONf_chiral_restr0.0589418
X-RAY DIFFRACTIONf_plane_restr0.011986
X-RAY DIFFRACTIONf_dihedral_angle_d25.17211244
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.763247744341 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.410.40621020.4022255X-RAY DIFFRACTION80.33
2.41-2.750.41451670.36862748X-RAY DIFFRACTION98.51
2.75-3.470.35451420.29112764X-RAY DIFFRACTION96.67
3.47-34.090.22821540.18943027X-RAY DIFFRACTION99.44
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)
11.396364558340.005335658447120.5212423095735.160761179180.8787406739042.111916686240.330507214742-0.373899328578-0.142350610011-0.62705469664-0.3564145447760.167180166533-0.0736148111419-0.391498439373-0.02587864832220.3623371815910.0914377394594-0.04195002832360.870897769058-0.07320851874160.4462728163495.647702188292.0275939349395.361782471
20.531495006982-0.0835013513862-0.2845452348320.6827647868761.086751527532.07044099671-0.249849573071-0.568996907421-0.0694053849748-0.8446431996280.457779158517-0.104135381435-0.5335232065810.144100829711-0.1767924119740.8346755947790.0588517106172-0.01235091845890.601975821570.01629367668380.4572933019515.45179189817-0.61492610247776.0503565269
32.58060755945-0.377977469448-0.9583112305950.108386115262-0.06076531167391.02141675877-0.177549295404-1.08517153727-0.179822296764-0.4696499525480.220254827444-0.08826281268040.1238542298620.1804685012910.09420042135290.7024773210820.08938565003610.06678562067510.603970000640.02358556468990.448055821863-3.9838653323725.555840297178.1670230151
41.279946864830.208631134929-1.186454193751.85244191315-0.9345187092513.358016435810.0080480055809-0.445961292256-0.147169928955-0.78154006764-0.1283415394730.08400323205220.1187926498620.7654039608110.07105780174980.6430594128640.10256341424-0.03549504209740.62859823754-0.04248560204890.437830179918-7.1250953891325.581547371674.9216750712
53.05538371307-1.31822970277-0.1502019484431.98999392141-2.17484426353.551698582320.414156267325-0.195039825661-0.2572363443750.123605218140.06210228684980.0879302989902-0.338595116670.403369059151-0.4285425261911.037961412370.00311595049956-0.0631060377770.309869450667-0.03850775487810.3646286248281.52870665628-2.5247008638268.0814840078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )AB2 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 37 )AB22 - 37
3X-RAY DIFFRACTION3chain 'B' and (resid -3 through 16 )BE-3 - 16
4X-RAY DIFFRACTION4chain 'B' and (resid 17 through 37 )BE17 - 37
5X-RAY DIFFRACTION5chain 'A' and (resid -3 through 1 )AB-3 - 1

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