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- PDB-6wjr: Apo structure of the FMN riboswitch aptamer domain in the presenc... -

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Basic information

Entry
Database: PDB / ID: 6wjr
TitleApo structure of the FMN riboswitch aptamer domain in the presence of sulfate
ComponentsRNA (112-MER)
KeywordsRNA / riboswitch / RNA conformation / apo
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWilt, H.M. / Wang, Y.-X. / Stagno, J.R.
CitationJournal: J Struct Biol X / Year: 2020
Title: FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations.
Authors: Wilt, H.M. / Yu, P. / Tan, K. / Wang, Y.X. / Stagno, J.R.
History
DepositionApr 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Structure summary / Category: audit_author
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: RNA (112-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3503
Polymers36,2291
Non-polymers1202
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.635, 36.468, 205.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: RNA chain RNA (112-MER)


Mass: 36229.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria) / References: GenBank: 929732263
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, and 26 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 2.7→42.14 Å / Num. obs: 15928 / % possible obs: 99 % / Redundancy: 4.046 % / Biso Wilson estimate: 104.085 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.104 / Χ2: 0.834 / Net I/σ(I): 8.16 / Num. measured all: 64444
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.774.2944.7930.335015117311680.1385.44799.6
2.77-2.854.2813.0270.514825113211270.233.44299.6
2.85-2.934.1552.3360.74508108610850.252.67299.9
2.93-3.023.9321.4091.14239108410780.4871.61799.4
3.02-3.124.1640.8161.94272102710260.7930.93399.9
3.12-3.234.2810.4393.334281100210000.940.599.8
3.23-3.354.310.2844.75429710019970.9770.32399.6
3.35-3.494.3220.2635.4939379139110.9780.399.8
3.49-3.644.1190.1946.637699249150.980.22399
3.64-3.824.2150.143935708498470.9880.16499.8
3.82-4.023.8660.11910.5431978378270.9870.13998.8
4.02-4.273.7690.09912.8128837747650.9840.11798.8
4.27-4.563.6160.08414.5827777787680.990.09898.7
4.56-4.934.0060.06917.7926686736660.9920.08199
4.93-5.44.0060.06619.4225206466290.9930.07697.4
5.4-6.043.9210.06220.3722825955820.9930.07297.8
6.04-6.973.8050.05520.7419715295180.9940.06497.9
6.97-8.543.3750.04920.9314854554400.9910.05996.7
8.54-12.073.470.04422.3212843813700.9950.05297.1
12.07-42.143.1770.04321.586642332090.9990.05189.7

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Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F2Q

3f2q


Resolution: 2.7→42.14 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 727 4.67 %
Rwork0.2206 14853 -
obs0.2222 15580 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 261.26 Å2 / Biso mean: 118.0549 Å2 / Biso min: 66.8 Å2
Refinement stepCycle: final / Resolution: 2.7→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2382 6 2 2390
Biso mean--90.13 76.52 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062671
X-RAY DIFFRACTIONf_angle_d1.3854165
X-RAY DIFFRACTIONf_dihedral_angle_d16.6581329
X-RAY DIFFRACTIONf_chiral_restr0.096555
X-RAY DIFFRACTIONf_plane_restr0.008111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80.5857600.47321249130982
2.8-2.910.4808730.464614711544100
2.91-3.040.3635900.38021500159099
3.04-3.20.245680.275914791547100
3.2-3.40.2559590.26271491155099
3.4-3.660.2527830.22791502158599
3.66-4.030.3014750.22041497157299
4.03-4.620.1723790.19261509158899
4.62-5.810.1989770.1821530160799
5.81-42.140.3002630.20351625168896
Refinement TLS params.Method: refined / Origin x: 11.14 Å / Origin y: -14.882 Å / Origin z: -30.679 Å
111213212223313233
T1.0823 Å20.0257 Å20.1485 Å2-0.9913 Å20.1038 Å2--0.9917 Å2
L2.9108 °20.9563 °2-0.6492 °2-2.8371 °2-0.2562 °2--2.072 °2
S0.2585 Å °-0.8568 Å °0.4733 Å °0.7003 Å °-0.01 Å °0.5371 Å °-0.3282 Å °-0.0992 Å °0.0001 Å °
Refinement TLS groupSelection details: ( CHAIN X AND RESID 1:111 )

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