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- PDB-7wia: The apo-form of THF-II C22G riboswitch -

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Basic information

Entry
Database: PDB / ID: 7wia
TitleThe apo-form of THF-II C22G riboswitch
ComponentsRNA (50-MER)
KeywordsRNA / apo form
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 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)


Theoretical massNumber of molelcules
Total (without water)16,3281
Polymers16,3281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.420, 66.420, 93.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain RNA (50-MER)


Mass: 16327.617 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)
Has ligand of interestN

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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: 66.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20mM HEPES pH7.5, 20-25% PEG 3350

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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: 3.05→50 Å / Num. obs: 4001 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.961 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.156 / Χ2: 0.057 / Net I/σ(I): 6.6 / Num. measured all: 80579
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.05-3.17.40.9544441.101199.6
3.1-3.167.90.894421.131199.8
3.16-3.228.40.8814421.113199.8
3.22-3.299.60.6234571.3681100
3.29-3.369.80.5184361.1481100
3.36-3.439.90.6074461.1471100
3.43-3.5210.10.6314511.2871100
3.52-3.6210.20.514391.151100
3.62-3.7210.10.3934631.4391100
3.72-3.84100.3344421.1771100
3.84-3.989.10.3994531.471100
3.98-4.1490.2284281.1391100
4.14-4.339.20.2214391.181100
4.33-4.569.70.2044421.1571100
4.56-4.849.60.1974541.1551100
4.84-5.2190.1514391.0661100
5.21-5.7480.1334511.3371100
5.74-6.577.70.1154391.193199.8
6.57-8.278.70.0914670.869199.6
8.27-507.40.1044430.885199.6

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WI9

7wi9


Resolution: 3.22→18.13 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 196 4.91 %
Rwork0.1698 --
obs0.1716 3991 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.22→18.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1082 0 0 1082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011209
X-RAY DIFFRACTIONf_angle_d0.4491887
X-RAY DIFFRACTIONf_dihedral_angle_d11.243611
X-RAY DIFFRACTIONf_chiral_restr0.025252
X-RAY DIFFRACTIONf_plane_restr0.00250
LS refinement shellResolution: 3.22→3.34 Å
RfactorNum. reflection% reflection
Rfree0.23 --
Rwork0.172 --
obs-323 100 %

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