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- PDB-9v4v: Crystal structure of Guanine-II riboswitch in complex with isoxan... -

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Basic information

Entry
Database: PDB / ID: 9v4v
TitleCrystal structure of Guanine-II riboswitch in complex with isoxanthopterin
ComponentsRNA (71-MER)
KeywordsRNA / guanine riboswitch
Function / homology2-aminopteridine-4,7(3H,8H)-dione / RNA / RNA (> 10)
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,1663
Polymers22,9621
Non-polymers2032
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.967, 48.962, 120.526
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-203-

HOH

21A-210-

HOH

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Components

#1: RNA chain RNA (71-MER)


Mass: 22962.490 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-7PD / 2-aminopteridine-4,7(3H,8H)-dione / isoxanthopterin


Mass: 179.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
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: 3.12→60.26 Å / Num. obs: 4140 / % possible obs: 94.3 % / Redundancy: 10.9 % / CC1/2: 0.977 / Net I/σ(I): 7.2
Reflection shellResolution: 3.12→3.29 Å / Num. unique obs: 610 / CC1/2: 0.981

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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: 3.12→60.26 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2963 404 9.99 %
Rwork0.2422 --
obs0.2473 4043 92.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.12→60.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1520 14 18 1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021711
X-RAY DIFFRACTIONf_angle_d0.7272662
X-RAY DIFFRACTIONf_dihedral_angle_d20.391851
X-RAY DIFFRACTIONf_chiral_restr0.037354
X-RAY DIFFRACTIONf_plane_restr0.00472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.570.39371240.32151127X-RAY DIFFRACTION89
3.57-4.50.32251270.26361138X-RAY DIFFRACTION88
4.5-60.260.25271530.20891374X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.9744 Å / Origin y: 11.0585 Å / Origin z: 29.0069 Å
111213212223313233
T0.4893 Å20.0575 Å2-0.1832 Å2-0.4172 Å20.0592 Å2--0.5285 Å2
L4.5731 °2-0.5601 °2-0.4025 °2-2.7881 °2-0.1418 °2--1.7497 °2
S-0.2095 Å °-0.4451 Å °0.2579 Å °0.6445 Å °0.3911 Å °-0.2697 Å °-0.5374 Å °0.2043 Å °-0.1245 Å °
Refinement TLS groupSelection details: all

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