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- PDB-9v4x: Crystal structure of Guanine-II riboswitch in complex with 8-azag... -

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Basic information

Entry
Database: PDB / ID: 9v4x
TitleCrystal structure of Guanine-II riboswitch in complex with 8-azaguanine
ComponentsRNA (71-MER)
KeywordsRNA / guanine riboswitch
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsLi, H.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Ligand specificity and adaptability revealed by the first Guanine-II riboswitch tertiary structure.
Authors: Li, H. / Shen, X. / Xu, X. / Tai, X. / He, M. / Zhang, J. / Ren, A.
History
DepositionMay 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9552
Polymers22,8031
Non-polymers1521
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.885, 48.991, 120.122
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222
Components on special symmetry positions
IDModelComponents
11A-208-

HOH

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Components

#1: RNA chain RNA (71-MER)


Mass: 22802.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-9QC / 5-azanyl-3,6-dihydro-[1,2,3]triazolo[4,5-d]pyrimidin-7-one


Mass: 152.114 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.52 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.08 M sodium chloride, 0.04 M sodium cacodylate trihydrate (pH 7.0), 30% v/v (+/-)-2-methyl-2,4-pentanediol, and 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: 1.10213 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10213 Å / Relative weight: 1
ReflectionResolution: 2.92→60.06 Å / Num. obs: 4941 / % possible obs: 93.8 % / Redundancy: 11.4 % / CC1/2: 0.977 / Net I/σ(I): 7.6
Reflection shellResolution: 2.92→3.08 Å / Num. unique obs: 736 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→45.36 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 483 10.01 %
Rwork0.2043 --
obs0.2101 4825 91.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.92→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1511 11 9 1531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051701
X-RAY DIFFRACTIONf_angle_d1.1362646
X-RAY DIFFRACTIONf_dihedral_angle_d19.12859
X-RAY DIFFRACTIONf_chiral_restr0.055355
X-RAY DIFFRACTIONf_plane_restr0.00677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.340.33751600.26261443X-RAY DIFFRACTION95
3.34-4.210.30591390.231246X-RAY DIFFRACTION80
4.21-45.360.22931840.17541653X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.9529 Å / Origin y: 11.2577 Å / Origin z: 28.6518 Å
111213212223313233
T0.7143 Å20.0501 Å2-0.1176 Å2-0.5789 Å20.0736 Å2--0.3647 Å2
L4.1332 °2-1.1784 °20.4676 °2-2.7441 °2-0.1648 °2--0.5389 °2
S-0.4034 Å °-0.4553 Å °0.1579 Å °0.7408 Å °0.355 Å °-0.1013 Å °-0.6801 Å °0.1281 Å °0.0663 Å °
Refinement TLS groupSelection details: all

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