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- PDB-7wib: The THF-II riboswitch bound to THF -

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Basic information

Entry
Database: PDB / ID: 7wib
TitleThe THF-II riboswitch bound to THF
ComponentsRNA (50-MER)
KeywordsRNA / THF-II riboswitch / THF
Function / homology(6S)-5,6,7,8-TETRAHYDROFOLATE / RNA / RNA (> 10)
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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)16,7332
Polymers16,2881
Non-polymers4451
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint4 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.623, 66.623, 89.967
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
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: 3.56 Å3/Da / Density % sol: 65.41 %
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: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→50 Å / Num. obs: 5768 / % possible obs: 99.8 % / Redundancy: 8.1 % / Biso Wilson estimate: 85.84 Å2 / CC1/2: 0.938 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.115 / Χ2: 0.047 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.85-2.98.90.8375411.0771100
2.9-2.9590.5675381.274199.8
2.95-3.0190.3865181.5271100
3.01-3.078.70.2424991.675199.8
3.07-3.148.70.235681.3931100
3.14-3.218.50.2025021.4821100
3.21-3.297.40.1515331.5521100
3.29-3.388.80.1475351.5131100
3.38-3.489.10.175111.3211100
3.48-3.598.80.1495291.3071100
3.59-3.728.60.125181.3841100
3.72-3.878.40.1185301.3861100
3.87-4.048.10.1215271.4461100
4.04-4.267.30.1085181.1661100
4.26-4.527.40.1025371.201199.8
4.52-4.877.60.1015131.216199.6
4.87-5.367.40.0925451.2031100
5.36-6.146.90.095191.189199.6
6.14-7.736.80.085271.0241100
7.73-505.80.0915291.253198.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WI9

7wi9


Resolution: 2.83→28.85 Å / SU ML: 0.0814 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 283 4.96 %
Rwork0.2013 5424 -
obs0.2028 5707 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 105.86 Å2
Refinement stepCycle: LAST / Resolution: 2.83→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1075 13 0 1088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00151215
X-RAY DIFFRACTIONf_angle_d0.49071893
X-RAY DIFFRACTIONf_chiral_restr0.0215252
X-RAY DIFFRACTIONf_plane_restr0.001851
X-RAY DIFFRACTIONf_dihedral_angle_d10.0101612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-3.560.3271370.27192593X-RAY DIFFRACTION96.13
3.56-28.850.20441460.1842831X-RAY DIFFRACTION99.53

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