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- PDB-8khh: Crystal structure of 2'-dG-III riboswitch with guanosine -

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Basic information

Entry
Database: PDB / ID: 8khh
TitleCrystal structure of 2'-dG-III riboswitch with guanosine
ComponentsRNA (71-MER)
KeywordsRNA / Riboswitch / 2'-Deoxyguanosine / 2'-dG / Guanosine / Aptamer
Function / homologyGUANOSINE / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiao, W. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family.
Authors: Chen, K. / Liao, W. / Wang, J. / Ren, Y. / Lu, Z. / Peng, X. / Wang, J. / Huang, L.
History
DepositionAug 21, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (71-MER)
B: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,21013
Polymers45,4372
Non-polymers77311
Water19811
1
A: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1408
Polymers22,7181
Non-polymers4217
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0715
Polymers22,7181
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.727, 58.621, 57.182
Angle α, β, γ (deg.)90.000, 96.675, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 through 2 and (name P...
d_2ens_1(chain "B" and ((resid 1 through 2 and (name P...

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_11GGCCAA1 - 61 - 6
d_12GMPGMPGMPGMPAC101
d_21GGCCBB1 - 61 - 6
d_22GMPGMPGMPGMPBJ101

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Components

#1: RNA chain RNA (71-MER)


Mass: 22718.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus sp. (bacteria)
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.08 M Sodium chloride, 0.01 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 6.4, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine ...Details: 0.08 M Sodium chloride, 0.01 M Potassium chloride, 0.01 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 6.4, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride, 0.1M Glycine.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.3→68.89 Å / Num. obs: 20324 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 55.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.048 / Net I/σ(I): 10.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.902 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2853 / CC1/2: 0.33 / Rpim(I) all: 1.149 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→31.1 Å / SU ML: 0.4479 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 1007 4.97 %
Rwork0.2381 19270 -
obs0.2388 20277 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3010 49 11 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523408
X-RAY DIFFRACTIONf_angle_d0.75395298
X-RAY DIFFRACTIONf_chiral_restr0.0324718
X-RAY DIFFRACTIONf_plane_restr0.0059144
X-RAY DIFFRACTIONf_dihedral_angle_d12.74971698
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.58653069921 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.44031360.4152612X-RAY DIFFRACTION94.47
2.42-2.570.35941380.36352747X-RAY DIFFRACTION99.97
2.57-2.770.36461230.3522782X-RAY DIFFRACTION99.86
2.77-3.050.35661600.34122750X-RAY DIFFRACTION100
3.05-3.490.28221500.25712754X-RAY DIFFRACTION99.79
3.49-4.40.22821480.20362781X-RAY DIFFRACTION99.86
4.4-31.10.17721520.16912844X-RAY DIFFRACTION99.73
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)
12.80455723601-0.384001675443.946759909722.201949527340.9392393238996.85513189929-0.7488140013810.3615714566260.5961048566760.94384085-0.06737671230051.14384791306-0.3248184579960.8804750121770.5260124200720.440902028749-0.0660142188365-0.2210738575280.7395212806090.04026023513330.9051601130948.2990014403832.244695544616.0725241264
21.77068716971-1.05300323914-0.09055985961314.093846212750.4027027871210.6269114783820.02978205425690.152057931706-0.11044452908-0.3484249443410.0274153293484-0.07731888797050.18490723366-0.0846828945733-0.11883113270.623910739381-0.007963942414030.1007627687660.4310656459070.006348425065050.2639912899130.521158974717.411172263423.8490735673
30.9557677793021.635759531810.04603463179043.97400626218-0.8789246966292.44412105246-0.5584770729840.1671594634380.331833595328-0.4148651698610.3408577535570.139779288055-0.0994023959545-0.1022382183280.1118976448020.4997986537530.04640578241650.02110498534260.39693037288-0.005529753592340.18932368667527.289244160229.613669885518.0556706761
43.975877015183.48738094578-0.3695507291978.3603802567-3.384975287682.02212410704-0.0652377561512-0.180873920433-0.03741148343960.159134307172-0.3644964783230.739450886768-0.1336181547360.2729051737240.4379218166770.647246537038-0.1998046633960.3142424481150.652539856315-0.003326949712310.661814277873.4947273236512.179940685147.064024831
54.548275198911.513763790211.774290464112.455633557011.373778778012.635231727420.08204903020270.0631687546487-0.2538865576660.2350748342990.148574063243-0.02123854207830.0612012690543-0.00644548622249-0.1827498413410.5260161492110.004629122474440.01881219590050.411909670969-0.02152176018080.28394615220422.800708685930.318588362949.9221987713
61.06964824577-1.79432677576-0.7774357857713.259801644810.7478086830561.89365339256-0.403268734581-0.105570437363-0.01173841488030.2820165575810.389262861344-0.06141322889920.3235519399190.102935012538-0.05321630639530.482470697343-0.05212411287780.06278855466080.427162666124-0.00343658689190.26113396491522.203505569217.322440363546.5174606967
71.87017357371-2.771987575172.203971258644.29192767412-3.488022275822.95644064942-0.0483655542356-0.0931196044024-0.3111038503410.427867903215-0.02788200055-0.4581278334130.630333565423-0.1872965957880.1213022713292.64180860328-0.135875362950.2374958638311.2956092159-0.2615168812762.32623989527-5.007608502-0.72830060258654.8816546712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 40 )AA11 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 71 )AA41 - 71
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )BC1 - 10
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 40 )BC11 - 40
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 70 )BC41 - 70
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 71 )BC71

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