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- PDB-9m6b: Crystal structure of xanthine/guanine RNA (P1-12bp) aptamer with ... -

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Basic information

Entry
Database: PDB / ID: 9m6b
TitleCrystal structure of xanthine/guanine RNA (P1-12bp) aptamer with guanine
ComponentsRNA (42-MER)
KeywordsRNA / xanthine/guanine RNA aptamer / guanine
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / GUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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

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Assembly

Deposited unit
A: RNA (42-MER)
B: RNA (42-MER)
C: RNA (42-MER)
D: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,08112
Polymers53,8844
Non-polymers2,1978
Water2,270126
1
A: RNA (42-MER)
C: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2916
Polymers26,9422
Non-polymers1,3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (42-MER)
hetero molecules

D: RNA (42-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7906
Polymers26,9422
Non-polymers8484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)22.885, 46.687, 99.999
Angle α, β, γ (deg.)95.270, 95.470, 90.550
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: RNA chain
RNA (42-MER)


Mass: 13470.997 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


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


Mass: 151.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5O / 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.: 126 / 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: 1.97 Å3/Da / Density % sol: 37.41 %
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-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: 2.61→33.08 Å / Num. obs: 12213 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.12 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.166 / Net I/σ(I): 6.4
Reflection shellResolution: 2.62→2.69 Å / Rmerge(I) obs: 0.907 / Num. unique obs: 858 / CC1/2: 0.288 / Rpim(I) all: 0.907 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→24.78 Å / SU ML: 0.3626 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.9141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3041 596 4.93 %
Rwork0.2358 11490 -
obs0.2388 12086 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.07 Å2
Refinement stepCycle: LAST / Resolution: 2.61→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3503 137 126 3766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274052
X-RAY DIFFRACTIONf_angle_d0.65476300
X-RAY DIFFRACTIONf_chiral_restr0.0331837
X-RAY DIFFRACTIONf_plane_restr0.0043172
X-RAY DIFFRACTIONf_dihedral_angle_d13.91722008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.880.3971700.3122819X-RAY DIFFRACTION95.62
2.88-3.290.33511420.25442886X-RAY DIFFRACTION97.71
3.29-4.140.2931510.22522838X-RAY DIFFRACTION97.84
4.14-24.780.24141330.20382947X-RAY DIFFRACTION98.47

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