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- PDB-7wif: The THF-II riboswitch bound to H4B -

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Basic information

Entry
Database: PDB / ID: 7wif
TitleThe THF-II riboswitch bound to H4B
ComponentsRNA (50-MER)
KeywordsRNA / Holo form
Function / homology5,6,7,8-TETRAHYDROBIOPTERIN / RNA / RNA (> 10)
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 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)16,5292
Polymers16,2881
Non-polymers2411
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint3 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.226, 66.226, 92.793
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-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N5O3 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
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 6M / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 5787 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 80.59 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.094 / Χ2: 0.035 / Net I/σ(I): 11.8 / Num. measured all: 85703
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.85-2.910.10.5595381.0211100
2.9-2.959.90.4355041.1131100
2.95-3.019.20.2695601.3571100
3.01-3.078.70.2165221.2531100
3.07-3.148.70.1875191.3431100
3.14-3.218.60.1694961.2341100
3.21-3.298.60.1425601.3341100
3.29-3.388.60.1325001.2831100
3.38-3.488.70.1345531.2711100
3.48-3.598.20.1235241.4111100
3.59-3.727.60.115190.9831100
3.72-3.877.40.1055440.9681100
3.87-4.046.90.0985131.0811100
4.04-4.256.90.0975261.1071100
4.25-4.527.30.0875211.09199.8
4.52-4.877.40.0855261.1071100
4.87-5.367.20.0835250.9831100
5.36-6.126.90.0765370.9411100
6.12-7.697.60.085330.91100
7.69-307.90.0755340.838199.8

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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: 2.86→28.68 Å / SU ML: 0.2921 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6659
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 566 9.88 %
Rwork0.1915 5165 -
obs0.1938 5731 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.64 Å2
Refinement stepCycle: LAST / Resolution: 2.86→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1079 17 0 1096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021223
X-RAY DIFFRACTIONf_angle_d0.59531906
X-RAY DIFFRACTIONf_chiral_restr0.0267255
X-RAY DIFFRACTIONf_plane_restr0.003251
X-RAY DIFFRACTIONf_dihedral_angle_d10.9554628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-3.140.4191320.33711244X-RAY DIFFRACTION96.83
3.14-3.60.27441460.21471265X-RAY DIFFRACTION99.86
3.6-4.530.24771400.2221288X-RAY DIFFRACTION99.65
4.53-28.680.16151480.15021368X-RAY DIFFRACTION99.87

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