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- PDB-8xzo: Crystal structure of folE riboswitch with Guanine -

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Basic information

Entry
Database: PDB / ID: 8xzo
TitleCrystal structure of folE riboswitch with Guanine
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch / Guanine
Function / homologyGUANINE / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLi, C.Y. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structure-based characterization and compound identification of the wild-type THF class-II riboswitch.
Authors: Li, C. / Xu, X. / Geng, Z. / Zheng, L. / Song, Q. / Shen, X. / Wu, J. / Zhao, J. / Li, H. / He, M. / Tai, X. / Zhang, L. / Ma, J. / Dong, Y. / Ren, A.
History
DepositionJan 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (53-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6257
Polymers17,1741
Non-polymers4516
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.018, 57.795, 62.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (53-MER) / env6


Mass: 17174.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified eubacterium clone A70 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.58 %
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 MPD, 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 PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.26→37.82 Å / Num. obs: 34010 / % possible obs: 67.4 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.056 / Χ2: 0.75 / Net I/σ(I): 12.2 / Num. measured all: 367905
Reflection shellResolution: 1.26→1.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.603 / Num. unique obs: 1286 / CC1/2: 0.303 / Rpim(I) all: 0.79 / Rrim(I) all: 0.199 / Χ2: 0.64

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→26.23 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1214 9.9 %
Rwork0.2094 --
obs0.2126 12267 91.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→26.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1104 61 24 1189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051290
X-RAY DIFFRACTIONf_angle_d1.0721999
X-RAY DIFFRACTIONf_dihedral_angle_d14.941646
X-RAY DIFFRACTIONf_chiral_restr0.042264
X-RAY DIFFRACTIONf_plane_restr0.00654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.35071450.28311301X-RAY DIFFRACTION100
2.04-2.140.3364900.2856808X-RAY DIFFRACTION61
2.14-2.240.3361320.28861265X-RAY DIFFRACTION100
2.26-2.390.27331360.2891156X-RAY DIFFRACTION100
2.39-2.570.32131510.30341318X-RAY DIFFRACTION100
2.57-2.830.37551160.32721170X-RAY DIFFRACTION87
2.83-3.240.3151500.25641335X-RAY DIFFRACTION100
3.24-4.080.22481380.18581260X-RAY DIFFRACTION92
4.08-26.230.1571560.14071440X-RAY DIFFRACTION100

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