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- PDB-8xzn: Crystal structure of folE riboswitch with BH4 -

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Basic information

Entry
Database: PDB / ID: 8xzn
TitleCrystal structure of folE riboswitch with BH4
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch / BH4
Function / homology5,6,7,8-TETRAHYDROBIOPTERIN / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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)17,6665
Polymers17,1741
Non-polymers4924
Water52229
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)49.277, 57.490, 62.914
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-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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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.: 29 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
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: 1.82→50 Å / Num. obs: 16566 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.024 / Rrim(I) all: 0.084 / Χ2: 1.029 / Net I/σ(I): 6 / Num. measured all: 210385
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.82-1.8511.81.1118040.7340.920.331.1610.42599.8
1.85-1.8912.70.8848160.8610.9620.2540.920.457100
1.89-1.9212.80.8197960.8670.9640.2340.8520.57299.9
1.92-1.9613.10.6358130.9220.9790.180.6610.475100
1.96-212.90.4468250.9560.9890.1270.4640.48499.9
2-2.05120.3858220.9560.9890.1150.4030.52299.6
2.05-2.112.90.3738030.9630.9910.1080.3890.67100
2.1-2.1613.40.2678220.9820.9950.0750.2780.569100
2.16-2.2213.50.228120.9870.9970.0610.2290.592100
2.22-2.2913.20.2158220.9910.9980.0610.2240.717100
2.29-2.37130.1588180.9940.9990.0450.1640.672100
2.37-2.4712.30.1328160.9930.9980.0390.1380.74599.8
2.47-2.5812.60.1178290.9940.9980.0340.1220.903100
2.58-2.7213.50.1078280.9950.9990.030.1111.14100
2.72-2.8913.20.0938310.9960.9990.0270.0971.248100
2.89-3.1112.80.0818240.9970.9990.0240.0841.574100
3.11-3.4312.10.0748430.9980.9990.0220.0781.98399.6
3.43-3.9213.10.0738480.9980.9990.0210.0772.15299.9
3.92-4.9411.80.0728670.9960.9990.0220.0752.19899.8
4.94-5011.60.0739270.9950.9990.0230.0772.37799.7

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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: 1.82→31.46 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 851 5.16 %
Rwork0.2149 --
obs0.2162 16502 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→31.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1104 65 29 1198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061296
X-RAY DIFFRACTIONf_angle_d1.1872008
X-RAY DIFFRACTIONf_dihedral_angle_d15.192653
X-RAY DIFFRACTIONf_chiral_restr0.047267
X-RAY DIFFRACTIONf_plane_restr0.00754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.940.34021420.31512542X-RAY DIFFRACTION99
1.94-2.080.33741190.28752578X-RAY DIFFRACTION100
2.08-2.290.31861430.29032596X-RAY DIFFRACTION100
2.29-2.630.27611440.28752584X-RAY DIFFRACTION100
2.63-3.310.27741510.25832617X-RAY DIFFRACTION100
3.31-31.460.20781520.16782734X-RAY DIFFRACTION99

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