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- PDB-9m6d: Crystal structure of xanthine/guanine RNA aptamer (P1-12bp) with ... -

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Basic information

Entry
Database: PDB / ID: 9m6d
TitleCrystal structure of xanthine/guanine RNA aptamer (P1-12bp) with 3-methylxanthine
ComponentsRNA (42-MER)
KeywordsRNA / 3-methylxanthine / xanthine/guanine RNA aptamer
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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)28,3447
Polymers26,9422
Non-polymers1,4025
Water93752
1
A: RNA (42-MER)
hetero molecules

B: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3447
Polymers26,9422
Non-polymers1,4025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Unit cell
Length a, b, c (Å)208.370, 22.600, 44.960
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 and (name C1" or name...

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_13I7UI7UI7UI7UAD102
d_21GTPGTPGTPGTPBF101
d_22CCCCBB-32
d_23I7UI7UI7UI7UBG102

NCS oper: (Code: givenMatrix: (0.992877908965, -0.00478083496625, 0.119040335627), (-0.00240912518642, -0.999795885063, -0.0200595196269), (0.119111938969, 0.0196298708312, -0.992686765383)Vector: -7. ...NCS oper: (Code: given
Matrix: (0.992877908965, -0.00478083496625, 0.119040335627), (-0.00240912518642, -0.999795885063, -0.0200595196269), (0.119111938969, 0.0196298708312, -0.992686765383)
Vector: -7.92837306481, -0.117638199097, -22.6618940362)

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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-I7U / 3-methyl-7~{H}-purine-2,6-dione / 3-Methylxanthine / 1076-22-8


Mass: 166.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 37.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.08 M Potassium chloride 0.02 M Magnesium chloride hexahydrate 50% 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: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.18→34.73 Å / Num. obs: 11974 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 47.71 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.065 / Net I/σ(I): 8.5
Reflection shellResolution: 2.18→2.24 Å / Rmerge(I) obs: 1.251 / Num. unique obs: 878 / CC1/2: 0.68 / Rpim(I) all: 0.561 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→30.56 Å / SU ML: 0.3033 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.6604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 599 5.05 %
Rwork0.2451 11274 -
obs0.2468 11873 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.64 Å2
Refinement stepCycle: LAST / Resolution: 2.18→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1740 89 52 1881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462034
X-RAY DIFFRACTIONf_angle_d1.09673164
X-RAY DIFFRACTIONf_chiral_restr0.0433418
X-RAY DIFFRACTIONf_plane_restr0.005486
X-RAY DIFFRACTIONf_dihedral_angle_d26.10111246
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.726050151458 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.40.34031550.31422745X-RAY DIFFRACTION100
2.4-2.750.38271430.33322765X-RAY DIFFRACTION99.97
2.75-3.460.30161300.27282792X-RAY DIFFRACTION98.65
3.46-30.560.24311710.20492972X-RAY DIFFRACTION99.65
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)
10.97335803443-0.5519427206891.16728645187-0.00792241991114-0.2720304297150.3654133567940.07627151978890.0420902020085-0.07315486810960.125505017468-0.1619912230910.3222208144490.008453626786830.3155150018190.1463564064870.4316251988050.0029268731110.0195000206880.46014820345-0.0257853713340.385666801331.8700136773.704988815571.58436670041
23.981810811390.0465916417704-0.0161550875172.2308749805-0.7345169352794.037697108-0.0549349149054-0.475927115219-0.374080069238-0.1985423305810.13402496892-0.4198807906590.1444841304510.09015609012880.01837017111420.406722929904-0.03958342187580.000522292080980.3949824955480.04754289111390.56206386322814.37568306116.310369285573.53479301134
32.28358973341-1.557940830951.93016458711.14215989649-0.8894427373722.54858340386-0.03003996609630.140794856455-0.3988880775210.2407743003520.02961064298790.267183733513-0.2464842385010.2194599091480.06057271191940.370597232205-0.03628069826330.03808137478450.3024715638490.03713501761180.33171801526543.94823079784.79828352884.47387755038
46.990305412570.310969971578-1.656808290270.714526124592-0.7711045443411.00262047802-0.690486118453-0.925405266646-0.0513781551884-0.1991428433260.409448750189-0.07490093886080.1418263692140.2738997453130.2512107640130.414853830288-0.09842473561670.04489146620790.61390525246-0.2308994206240.43445539288923.8569649043-3.87959750697-20.2712913571
57.732270045520.526705762987-4.418581201310.7959096591340.4303728009379.607084680750.2038254244720.09283237134071.39666355819-0.2095007532650.3669825570990.485440156699-1.88220154809-1.466665922-0.2169803846890.517287141995-0.227921427465-0.01643068725351.04172425104-0.1559963229020.5789364036464.36896732279-2.57800420809-28.6736412574
63.83164345491.86457033691-0.996311573603-0.407517516189-0.6007639226190.326056407241-0.444402596205-0.308236809479-0.0462002133454-0.1460994713750.1139490921120.2051985161960.0554852163633-0.1346403667120.2635062463820.418761806696-0.01490233374180.03526592633530.465534215431-0.09443828789590.57089270166522.5216255079-6.75759428428-22.1016420983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 11 )AB-3 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 26 )AB12 - 26
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 37 )AB27 - 37
4X-RAY DIFFRACTION4chain 'B' and (resid -3 through 11 )BE-3 - 11
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 16 )BE12 - 16
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 37 )BE17 - 37

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