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- PDB-9v4u: Crystal structure of Guanine-II riboswitch in complex with 7,8-di... -

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Basic information

Entry
Database: PDB / ID: 9v4u
TitleCrystal structure of Guanine-II riboswitch in complex with 7,8-dihydroneopterin
ComponentsRNA (71-MER)
KeywordsRNA / guanine riboswitch
Function / homologyChem-NPR / RNA / RNA (> 10)
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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)23,1064
Polymers22,8031
Non-polymers3043
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.933, 52.431, 218.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-NPR / 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE / 7,8-DIHYDRONEOPTERIN


Mass: 255.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.5 Å3/Da / Density % sol: 50.7 %
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: 1.10221 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10221 Å / Relative weight: 1
ReflectionResolution: 2.54→109.26 Å / Num. obs: 7622 / % possible obs: 100 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Net I/σ(I): 4.5
Reflection shellResolution: 2.54→2.68 Å / Num. unique obs: 1093 / CC1/2: 0.538 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXPHENIX 1.18.2-3874refinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→36.42 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 359 4.8 %
Rwork0.2266 --
obs0.2282 7479 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1511 20 36 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061708
X-RAY DIFFRACTIONf_angle_d1.1662656
X-RAY DIFFRACTIONf_dihedral_angle_d17.348854
X-RAY DIFFRACTIONf_chiral_restr0.046357
X-RAY DIFFRACTIONf_plane_restr0.00672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.54-2.910.44281110.37892298X-RAY DIFFRACTION97
2.91-3.660.27321260.24742332X-RAY DIFFRACTION99
3.66-36.420.20971220.18112490X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.1419 Å / Origin y: -8.0137 Å / Origin z: -25.9581 Å
111213212223313233
T0.551 Å20.0131 Å2-0.0992 Å2-0.6472 Å20.0473 Å2--0.4154 Å2
L3.9113 °20.5369 °20.6197 °2-0.5772 °20.215 °2--3.435 °2
S-0.2427 Å °1.3064 Å °-0.0307 Å °-0.4107 Å °0.083 Å °0.1383 Å °-0.4167 Å °0.2479 Å °0.1029 Å °
Refinement TLS groupSelection details: all

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