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- PDB-8xzl: Crystal structure of folE riboswitch with DHF -

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Basic information

Entry
Database: PDB / ID: 8xzl
TitleCrystal structure of folE riboswitch with DHF
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch / DHF
Function / homologyDIHYDROFOLIC ACID / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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)17,9177
Polymers17,1741
Non-polymers7436
Water25214
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)48.904, 56.999, 62.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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)
#2: Chemical ChemComp-DHF / DIHYDROFOLIC ACID


Mass: 443.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N7O6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.29 %
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: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 10293 / % possible obs: 99.9 % / Redundancy: 11.9 % / CC1/2: 0.933 / CC star: 0.983 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Χ2: 1.701 / Net I/σ(I): 6.7 / Num. measured all: 122667
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.13-2.1710.70.8144920.8810.9680.2550.8540.562100
2.17-2.2111.10.7195170.9090.9760.2240.7540.54299.6
2.21-2.2511.40.7124850.9180.9780.2220.7460.955100
2.25-2.2911.20.7465080.910.9760.2330.7820.76799.8
2.29-2.3411.30.545140.9570.9890.1650.5650.884100
2.34-2.412.90.4764890.9670.9920.1390.4970.835100
2.4-2.46130.3975040.970.9920.1150.4140.8599.8
2.46-2.53130.3495150.9830.9960.1020.3630.931100
2.53-2.612.80.2975040.9760.9940.0880.311.091100
2.6-2.6812.50.2425040.9820.9950.0720.2521.289100
2.68-2.7811.70.2215040.9830.9960.0680.2321.51899.8
2.78-2.89120.1855200.990.9980.0570.1941.714100
2.89-3.0212.70.1415150.9960.9990.0430.1481.972100
3.02-3.1812.30.1195060.9930.9980.0390.1252.43499.8
3.18-3.3812.20.1075200.9960.9990.0340.1122.714100
3.38-3.64110.0975120.9960.9990.0320.1032.80499.8
3.64-4.0112.20.0955230.9930.9980.030.0992.926100
4.01-4.5912.40.0915260.9950.9990.0280.0952.946100
4.59-5.7811.30.0815480.9970.9990.0250.0852.659100
5.78-5010.70.0835870.9960.9990.0290.0893.25999.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→31.49 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 537 5.27 %
Rwork0.1993 --
obs0.1999 10188 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1104 82 14 1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051312
X-RAY DIFFRACTIONf_angle_d1.182029
X-RAY DIFFRACTIONf_dihedral_angle_d12.484655
X-RAY DIFFRACTIONf_chiral_restr0.04265
X-RAY DIFFRACTIONf_plane_restr0.00758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.350.39681340.31452340X-RAY DIFFRACTION98
2.35-2.690.33231360.30422356X-RAY DIFFRACTION99
2.69-3.380.25051340.26152416X-RAY DIFFRACTION100
3.38-31.490.17421330.16262539X-RAY DIFFRACTION100

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