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- PDB-8xze: Crystal structure of THF-II riboswitch with THF and soaked with Ir -

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Basic information

Entry
Database: PDB / ID: 8xze
TitleCrystal structure of THF-II riboswitch with THF and soaked with Ir
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch / THF
Function / homology: / SPERMINE / (6S)-5,6,7,8-TETRAHYDROFOLATE / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 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)18,49610
Polymers17,1741
Non-polymers1,3229
Water27015
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)50.276, 58.127, 62.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (53-MER) / env6


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)

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Non-polymers , 5 types, 24 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ir
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.44 %
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: 1.102 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 14592 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.033 / Rrim(I) all: 0.116 / Χ2: 0.554 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.35-2.3912.51.1783980.8630.9620.3421.2280.402
2.39-2.4312.81.2233870.8030.9440.3541.2740.396
2.43-2.4812.90.9073940.880.9680.260.9440.405
2.48-2.5312.80.853980.8840.9690.2440.8850.416
2.53-2.5912.50.6813900.9340.9830.1990.710.428
2.59-2.6511.70.5333920.9370.9840.1610.5570.438
2.65-2.7112.10.5193800.9440.9850.1550.5420.474
2.71-2.7912.40.4033990.9690.9920.1190.420.479
2.79-2.8713.60.3354010.9830.9960.0940.3480.474
2.87-2.9613.50.2593970.990.9980.0720.2690.48
2.96-3.0713.40.1934010.9960.9990.0540.2010.519
3.07-3.1913.30.1393990.9970.9990.0390.1450.59
3.19-3.33130.1133980.9970.9990.0320.1170.593
3.33-3.5112.80.1093930.99810.0310.1140.621
3.51-3.7311.90.0984000.9970.9990.030.1020.681
3.73-4.0211.50.0884080.9980.9990.0270.0920.679
4.02-4.42130.0814120.9980.9990.0230.0840.657
4.42-5.0612.90.0754190.99810.0210.0780.662
5.06-6.3712.10.0724250.9980.9990.0210.0750.705
6.37-5011.10.0764610.99810.0240.080.972

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→39.07 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 696 4.77 %
Rwork0.1974 --
obs0.1995 14592 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1136 53 15 1204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051312
X-RAY DIFFRACTIONf_angle_d1.0792029
X-RAY DIFFRACTIONf_dihedral_angle_d16.431660
X-RAY DIFFRACTIONf_chiral_restr0.041266
X-RAY DIFFRACTIONf_plane_restr0.00558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.520.36191180.33182744X-RAY DIFFRACTION97
2.52-2.780.35141450.29652780X-RAY DIFFRACTION99
2.78-3.180.32711710.26672761X-RAY DIFFRACTION99
3.18-40.22261320.18542805X-RAY DIFFRACTION100
4.01-39.070.18261300.14552806X-RAY DIFFRACTION99

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