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- PDB-8xzk: Crystal structure of folE riboswitch -

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Basic information

Entry
Database: PDB / ID: 8xzk
TitleCrystal structure of folE riboswitch
ComponentsRNA (53-MER)
KeywordsRNA / riboswitch
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesunidentified eubacterium clone A70 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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)


Theoretical massNumber of molelcules
Total (without water)17,0941
Polymers17,0941
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.282, 55.624, 61.903
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)


Mass: 17094.062 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.4 %
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: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.58→41.37 Å / Num. obs: 4721 / % possible obs: 89 % / Redundancy: 11.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Χ2: 1.02 / Net I/σ(I): 16.9 / Num. measured all: 55367
Reflection shellResolution: 2.58→2.72 Å / % possible obs: 25.4 % / Redundancy: 10.1 % / Rmerge(I) obs: 1.53 / Num. measured all: 1902 / Num. unique obs: 188 / CC1/2: 0.766 / Rpim(I) all: 0.477 / Rrim(I) all: 1.607 / Χ2: 0.72 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→36.55 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 461 10 %
Rwork0.199 --
obs0.2053 4609 87.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→36.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1132 0 4 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051261
X-RAY DIFFRACTIONf_angle_d1.11963
X-RAY DIFFRACTIONf_dihedral_angle_d13.958632
X-RAY DIFFRACTIONf_chiral_restr0.044264
X-RAY DIFFRACTIONf_plane_restr0.00653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.950.39471130.31931041X-RAY DIFFRACTION67
2.95-3.720.32351670.23411492X-RAY DIFFRACTION97
3.72-36.550.2141810.16481615X-RAY DIFFRACTION98

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