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- PDB-9m6a: Crystal structure of xanthine/guanine RNA aptamer (P1-12bp) with ... -

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Basic information

Entry
Database: PDB / ID: 9m6a
TitleCrystal structure of xanthine/guanine RNA aptamer (P1-12bp) with uric acid
ComponentsRNA (42-MER)
KeywordsRNA / xanthine/guanine RNA aptamer / uric acid
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / URIC ACID / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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)28,41710
Polymers26,9422
Non-polymers1,4758
Water1,04558
1
B: RNA (42-MER)
hetero molecules

A: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,41710
Polymers26,9422
Non-polymers1,4758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)22.657, 44.909, 207.198
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_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GTPGTPGTPGTPAC101
d_12CCCCAA-32
d_13URCURCURCURCAD102
d_21GTPGTPGTPGTPBF101
d_22CCCCBB-32
d_23URCURCURCURCBG102

NCS oper: (Code: givenMatrix: (-0.99990322707, 0.00502352609545, -0.0129730752518), (-0.00313993961749, -0.989958007407, -0.14132687059), (-0.0135527589487, -0.141272459302, 0.989877979838)Vector: 0. ...NCS oper: (Code: given
Matrix: (-0.99990322707, 0.00502352609545, -0.0129730752518), (-0.00313993961749, -0.989958007407, -0.14132687059), (-0.0135527589487, -0.141272459302, 0.989877979838)
Vector: 0.843597401607, 37.9792810143, -6.87126388245)

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Components

#1: RNA chain RNA (42-MER)


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


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.08 M Potassium chloride 0.02 M Magnesium chloride hexahydrate 52% 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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.52→207.2 Å / Num. obs: 7805 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 47.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.043 / Net I/σ(I): 11.2
Reflection shellResolution: 2.52→2.59 Å / Rmerge(I) obs: 0.623 / Num. unique obs: 525 / CC1/2: 0.864 / Rpim(I) all: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→51.8 Å / SU ML: 0.5028 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.303 344 4.47 %
Rwork0.247 7355 -
obs0.2494 7699 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.88 Å2
Refinement stepCycle: LAST / Resolution: 2.52→51.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1740 92 58 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022034
X-RAY DIFFRACTIONf_angle_d0.71333164
X-RAY DIFFRACTIONf_chiral_restr0.0312418
X-RAY DIFFRACTIONf_plane_restr0.003786
X-RAY DIFFRACTIONf_dihedral_angle_d25.79971246
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.732365927809 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-3.170.45351720.34753567X-RAY DIFFRACTION99.18
3.18-51.80.2481720.21043788X-RAY DIFFRACTION98.85
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)
12.052519460720.0254651192755-1.985048046661.58036683739-1.545785774623.682316807760.1571378092110.1728789765140.1516568570841.265628217041.050061352840.177462764083-1.181630023590.126187751512-0.8513595535290.8750700431250.0492136064031-0.08314948460780.622838446148-0.1268664450050.4422021951065.348023134570.86561557952973.4905827146
25.62840875644-2.590146571631.086731719436.79967059352.593728739216.528732388570.641327974586-0.4832712981440.5198276136530.187399220949-0.22125823087-0.0239203186804-0.495676846993-1.00704317723-0.4170958152250.4536643197090.101682273006-0.002013941791120.5735861527010.0816585126230.5525648339554.290650681811.2485865898298.6066437574
33.001306196452.43283907581-2.333736761693.61053524606-0.02532057839113.451374787960.3243645890210.159730890111-0.0447598842888-1.152221791580.5499584992370.0160284988024-0.681439347952-0.875191317078-0.6470111273040.645961205640.1635387438250.1173234604990.7332314775190.1269082267480.542419335284.127054693681.2465818330882.2017856827
42.88800247492-1.81047117127-1.839442611093.953822995520.3847496124253.895160728510.289401624045-0.520899094080.498437070233-0.4872438476850.117245835178-0.45350663917-1.25415026061.22336148538-0.2291528924550.580896732418-0.138955253781-0.01033414846130.566723455701-0.1349938494540.4432471179257.65801755453-2.9153767833761.6657748409
53.71683674726-0.2805498033420.07769803664140.708154787424-1.661673798073.711363266750.5756956489330.00479715394126-0.4225077932-0.0176609837752-0.313888347260.4643914680330.4826086675410.250897447105-0.1295704167670.483343146248-0.1139838650720.04544431030970.328051600749-0.08619091161550.440540585882-1.909698303531.408649697860.0126040299
61.6108578855-1.001147504450.5290308504892.80725730621-0.8592076428773.592549979750.01879838718830.1963063526710.3267173969940.05295315422750.172130394256-0.0454967519771-0.552360053104-0.0276846196713-0.2546331937180.4077052650780.01822139576250.003994868673980.3996788464770.04455554805290.456221717924-4.9994087196320.593186985878.1107526797
75.29183454357-0.782741351781-5.387533726028.494572102911.35167147566.53569052839-0.0358650357867-1.739334135870.5775323034130.6752422437540.291114927039-1.054167513370.08204253221391.9872249631-0.466502870130.442551065866-0.06037880841880.140023262070.588880584801-0.08287065831610.884090416875-2.7797738327130.176231107791.9879639226
83.093355885581.163271281721.42491018455.470117454420.6936864660622.27258882475-0.640341583526-0.21115881301-0.56806647604-0.6196600276380.3752058763510.2833421757690.0527362923449-0.7815543559010.3354277447240.2891180107710.1335351468020.1030156646430.503785649443-0.03350690587210.559500333861-8.3827950273824.205690708387.8410253768
95.01330742672-2.68488610668-0.7332029102514.6317506552-2.377641064597.87428673360.583156971640.04349151250740.646101037358-1.140963567650.0770698327408-0.0510552701994-0.01062766024332.13263697216-0.3668723033880.515232336298-0.0209487401684-0.002173238138930.613840062917-0.09657058130080.515293808107-2.1229898911121.300295482167.0717606156
108.460193198774.79739492436-3.175154100995.50122283991-1.784032474461.73758720543-0.6090420014090.967705538231-0.0427806664355-1.415427275440.2800803270580.2837312486291.0790099092-0.5375351522640.3783395145260.5456738566070.03202763202490.004825499266810.4420218025260.04919201751190.411378011462-7.6593033376832.011960272454.2081553082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 6 )AB-3 - 6
2X-RAY DIFFRACTION2chain 'A' and (resid 7 through 21 )AB7 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 31 )AB22 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 37 )AB32 - 37
5X-RAY DIFFRACTION5chain 'B' and (resid -3 through 1 )BE-3 - 1
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 11 )BE2 - 11
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 16 )BE12 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 26 )BE17 - 26
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 31 )BE27 - 31
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 37 )BE32 - 37

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