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- PDB-8xzr: Crystal structure of folE riboswitch with 8-NH2 Guanine -

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Basic information

Entry
Database: PDB / ID: 8xzr
TitleCrystal structure of folE riboswitch with 8-NH2 Guanine
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch / 8-NH2 Guanine
Function / homology8-AMINOGUANINE / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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)17,71310
Polymers17,1741
Non-polymers5399
Water91951
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)50.299, 58.590, 61.119
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)


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-ANG / 8-AMINOGUANINE


Mass: 166.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.7 Å3/Da / Density % sol: 54.47 %
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→32.37 Å / Num. obs: 33977 / % possible obs: 67.5 % / Redundancy: 10.4 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Rrim(I) all: 0.046 / Χ2: 0.72 / Net I/σ(I): 14.3 / Num. measured all: 354279
Reflection shellResolution: 1.26→1.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 3.183 / Num. unique obs: 1111 / CC1/2: 0.123 / Rpim(I) all: 2.373 / Rrim(I) all: 4.012 / Χ2: 0.62

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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: 1.83→25.15 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1342 9.9 %
Rwork0.2164 --
obs0.2197 13551 81.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1104 65 51 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051291
X-RAY DIFFRACTIONf_angle_d1.2172001
X-RAY DIFFRACTIONf_dihedral_angle_d17.591646
X-RAY DIFFRACTIONf_chiral_restr0.044264
X-RAY DIFFRACTIONf_plane_restr0.00654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.870.3161140.29021072X-RAY DIFFRACTION100
1.9-1.970.38991030.3201984X-RAY DIFFRACTION70
1.97-2.050.40371520.29491371X-RAY DIFFRACTION100
2.1-2.170.3636950.2963881X-RAY DIFFRACTION100
2.17-2.30.3426820.3252694X-RAY DIFFRACTION48
2.3-2.480.33371560.30731494X-RAY DIFFRACTION100
2.48-2.730.32941450.31311243X-RAY DIFFRACTION84
2.73-3.120.31081630.27541494X-RAY DIFFRACTION100
3.12-3.930.22711560.20411379X-RAY DIFFRACTION91
3.93-25.150.18451760.1491597X-RAY DIFFRACTION100

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