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- PDB-7wi9: The THF-II riboswitch bound to THF and soaking with SeUrea -

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Basic information

Entry
Database: PDB / ID: 7wi9
TitleThe THF-II riboswitch bound to THF and soaking with SeUrea
ComponentsRNA (50-MER)
KeywordsRNA / Holo form
Function / homologyselenourea / (6S)-5,6,7,8-TETRAHYDROFOLATE / RNA / RNA (> 10)
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.98 Å
AuthorsXu, L. / Fang, X. / Xiao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural insights into translation regulation by the THF-II riboswitch.
Authors: Xu, L. / Xiao, Y. / Zhang, J. / Fang, X.
History
DepositionJan 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
V: RNA (50-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2256
Polymers16,2881
Non-polymers9375
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.647, 66.647, 92.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: RNA chain RNA (50-MER)


Mass: 16287.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4N2Se / Feature type: SUBJECT OF INVESTIGATION
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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100mM sodium citrate, pH6.5, 1.5-2.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 9359 / % possible obs: 99.9 % / Redundancy: 18.9 % / Biso Wilson estimate: 83.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.111 / Net I/σ(I): 13.64
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.98-3.161.04415340.8991.0991
3.16-3.380.4313950.9820.4521
3.38-3.650.31213150.990.3291
3.65-40.18712240.9950.1971
4-4.460.12410980.9970.131
4.46-5.150.1059740.9960.1111
5.15-6.290.0778170.9970.0811
6.29-8.820.0566440.9990.0581
8.82-500.0463580.9990.0491

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.98→48.96 Å / SU ML: 0.1906 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 466 4.99 %
Rwork0.2113 8879 -
obs0.2124 9345 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.26 Å2
Refinement stepCycle: LAST / Resolution: 2.98→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1075 29 0 1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171227
X-RAY DIFFRACTIONf_angle_d0.51091905
X-RAY DIFFRACTIONf_chiral_restr0.0218252
X-RAY DIFFRACTIONf_plane_restr0.001855
X-RAY DIFFRACTIONf_dihedral_angle_d11.3309612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.410.30631520.28112937X-RAY DIFFRACTION99.58
3.42-4.30.28671530.23442976X-RAY DIFFRACTION99.87
4.31-48.960.19271610.18522966X-RAY DIFFRACTION99.84

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