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- PDB-8z8q: Crystal structure of 2'-dG riboswitch -

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Basic information

Entry
Database: PDB / ID: 8z8q
TitleCrystal structure of 2'-dG riboswitch
ComponentsRNA (71-MER)
KeywordsRNA / riboswitch / 2'-dG
Function / homology2'-DEOXY-GUANOSINE / RNA / RNA (> 10)
Function and homology information
Biological speciesPaenibacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsLiao, W. / Ren, Y. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: A general strategy for engineering GU base pairs to facilitate RNA crystallization.
Authors: Ren, Y. / Lin, X. / Liao, W. / Peng, X. / Deng, J. / Zhang, Z. / Zhan, J. / Zhou, Y. / Westhof, E. / Lilley, D.M.J. / Wang, J. / Huang, L.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: 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 (71-MER)
B: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9394
Polymers45,4052
Non-polymers5342
Water00
1
A: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9702
Polymers22,7021
Non-polymers2671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9702
Polymers22,7021
Non-polymers2671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.730, 51.275, 52.484
Angle α, β, γ (deg.)113.830, 114.990, 90.050
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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_11GGUUAA2 - 42 - 4
d_12GNGGNGGNGGNGAC101
d_21GGUUBB2 - 42 - 4
d_22GNGGNGGNGGNGBD101

NCS oper: (Code: givenMatrix: (0.999981131805, -0.00364334776324, -0.00494591253515), (-0.00364771000612, -0.999992965794, -0.000873255482255), (-0.00494269617117, 0.000891280260145, -0.999987387607) ...NCS oper: (Code: given
Matrix: (0.999981131805, -0.00364334776324, -0.00494591253515), (-0.00364771000612, -0.999992965794, -0.000873255482255), (-0.00494269617117, 0.000891280260145, -0.999987387607)
Vector: -22.3249994734, -4.40520835245, 15.5690392202)

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Components

#1: RNA chain RNA (71-MER)


Mass: 22702.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Paenibacillus (bacteria)
#2: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 7.0 30% v/v (+/-)-2-Methyl-2,4-pentanediol 0.012 ...Details: 0.04 M Lithium chloride, 0.08 M Strontium chloride hexahydrate, 0.02 M Magnesium chloride hexahydrate 0.04 M Sodium cacodylate trihydrate pH 7.0 30% 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: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.01→33.61 Å / Num. obs: 7298 / % possible obs: 97.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 70.75 Å2 / CC1/2: 0.957 / Net I/σ(I): 2.9
Reflection shellResolution: 3.01→3.09 Å / Num. unique obs: 538 / CC1/2: 0.779

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→27.34 Å / SU ML: 0.5723 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 52.0932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3271 362 5.15 %
Rwork0.3172 6661 -
obs0.3177 7023 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.05 Å2
Refinement stepCycle: LAST / Resolution: 3.01→27.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2922 38 0 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273308
X-RAY DIFFRACTIONf_angle_d0.73365140
X-RAY DIFFRACTIONf_chiral_restr0.0328696
X-RAY DIFFRACTIONf_plane_restr0.0051140
X-RAY DIFFRACTIONf_dihedral_angle_d15.34321650
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.315558276085 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.440.51331180.48172192X-RAY DIFFRACTION92.25
3.44-4.330.37411250.35192167X-RAY DIFFRACTION91.42
4.33-27.340.26261190.25292302X-RAY DIFFRACTION97.11
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)
11.63191253941-0.290337147453-0.6114027266271.250289836861.168613661631.15360444980.0619660282431-0.1545433575910.0856661467475-0.368108303419-0.01712330328530.03673166229410.106646375061-0.08434868552916.4090989177E-70.9686517168930.00591952035642-0.2802880823920.930781253968-0.05025191278821.7335989984811.6286481988-11.90990039246.07299804186
20.9077732158240.1747460862850.6489230119311.455301705421.234097692841.270579699530.1954670922470.1627558639080.6777826260520.09769084132770.1224748017040.5820599991460.0611243944125-0.01335690155990.001381953678420.844705425875-0.02935298391210.1886473073320.9419214116940.05285909411160.889860344024-10.68284737777.459495576239.43501827787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:70)AA2 - 70
2X-RAY DIFFRACTION2(chain B and resseq 2:70)BB2 - 70

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