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- PDB-8xzm: Crystal structure of folE riboswitch with DHN -

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Basic information

Entry
Database: PDB / ID: 8xzm
TitleCrystal structure of folE riboswitch with DHN
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch / DHN
Function / homologyChem-NPR / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)17,7538
Polymers17,1741
Non-polymers5797
Water61334
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)48.808, 57.085, 63.422
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NPR / 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE / 7,8-DIHYDRONEOPTERIN


Mass: 255.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 34 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
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: 1.98→50 Å / Num. obs: 12927 / % possible obs: 99.9 % / Redundancy: 11.6 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.041 / Rrim(I) all: 0.127 / Χ2: 2.265 / Net I/σ(I): 5.7 / Num. measured all: 149384
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.98-2.0112.40.6736140.9250.980.1970.7020.632100
2.01-2.0512.20.5596600.9550.9880.1670.5840.68399.8
2.05-2.0911.60.4916130.9050.9750.1510.5150.7999.8
2.09-2.13110.4626380.9320.9820.1430.4850.86699.8
2.13-2.1812.80.4316280.9470.9860.1250.4490.943100
2.18-2.23130.3826440.9680.9920.110.3971.05100
2.23-2.2912.90.3626350.9630.990.1050.3771.187100
2.29-2.3512.80.3086350.9760.9940.0910.3221.336100
2.35-2.4212.70.2846150.980.9950.0830.2961.484100
2.42-2.4912.60.266540.9770.9940.0760.2711.791100
2.49-2.5812.10.2416550.9760.9940.0730.2522.087100
2.58-2.69110.2086210.9860.9970.0670.2182.525100
2.69-2.8111.90.1966390.9890.9970.060.2052.86299.8
2.81-2.9612.30.1676560.9940.9990.0510.1753.138100
2.96-3.1411.70.1326420.9970.9990.0420.1393.691100
3.14-3.3910.80.1146520.9960.9990.0380.1214.15100
3.39-3.7310.10.1146550.9960.9990.0390.1214.40999.7
3.73-4.269.40.1086650.9940.9990.0380.1154.6699.7
4.26-5.379.90.1116780.9940.9980.0380.1174.529100
5.37-508.60.0917280.9970.9990.0340.0984.51299.5

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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: 1.98→28.54 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 638 4.96 %
Rwork0.2082 --
obs0.2096 12861 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1104 69 34 1207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041297
X-RAY DIFFRACTIONf_angle_d1.0882009
X-RAY DIFFRACTIONf_dihedral_angle_d12.615649
X-RAY DIFFRACTIONf_chiral_restr0.043266
X-RAY DIFFRACTIONf_plane_restr0.00754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.130.31441330.27192371X-RAY DIFFRACTION99
2.13-2.340.3521420.27442396X-RAY DIFFRACTION100
2.34-2.680.35861210.28652428X-RAY DIFFRACTION100
2.68-3.380.25461190.24992448X-RAY DIFFRACTION100
3.38-28.540.18381230.1652580X-RAY DIFFRACTION100

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