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

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Basic information

Entry
Database: PDB / ID: 6wjs
TitleApo structure of the FMN riboswitch aptamer domain in the presence of phosphate
ComponentsRNA (112-MER)
KeywordsRNA / riboswitch / RNA conformation / apo
Function / homologyPHOSPHATE ION / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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)36,3242
Polymers36,2291
Non-polymers951
Water00
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)73.579, 35.950, 203.088
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
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 / pH: 9
Details: 0.1 M SPG (succinic acid, sodium phosphate monobasic monohydrate, glycine; 2:7:7 ratio), pH 9.0, and 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.60747 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60747 Å / Relative weight: 1
ReflectionResolution: 3.8→41.79 Å / Num. obs: 5669 / % possible obs: 97.5 % / Redundancy: 3.09 % / Biso Wilson estimate: 133.182 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.177 / Χ2: 1.006 / Net I/σ(I): 5.16 / Num. measured all: 17520 / Scaling rejects: 5
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
3.8-3.93.2241.5270.8613704284250.1831.83299.3
3.9-4.013.2231.6550.7312894024000.2391.97899.5
4.01-4.123.2871.1791.0112593923830.3171.40897.7
4.12-4.253.2981.0861.1211843653590.4571.29798.4
4.25-4.393.1170.9811.2411973863840.411.17799.5
4.39-4.542.9590.7321.710773783640.6270.88196.3
4.54-4.712.9970.6911.799413223140.6480.8397.5
4.71-4.913.2510.5192.4211153473430.7690.62498.8
4.91-5.123.1240.3773.2510563413380.7980.45499.1
5.12-5.373.2120.3713.339412982930.870.44698.3
5.37-5.673.1530.3354.049302972950.8780.40499.3
5.67-6.013.1030.274.639002992900.8990.32597
6.01-6.423.1580.2016.097612532410.9690.2495.3
6.42-6.942.7060.1816.056442562380.9650.22293
6.94-7.63.0260.10610.127082362340.9850.12999.2
7.6-8.53.1050.08912.216522142100.9910.10898.1
8.5-9.812.8010.06714.555211931860.9940.08396.4
9.81-12.022.6350.034234481831700.9980.04292.9
12.02-172.6770.02430.133321331240.9990.0393.2
17-41.792.50.01532.3619590780.9990.01986.7

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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: 3.8→41.79 Å / SU ML: 0.77 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.93
RfactorNum. reflection% reflection
Rfree0.3275 258 4.57 %
Rwork0.2701 --
obs0.2724 5642 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.41 Å2 / Biso mean: 131.2073 Å2 / Biso min: 80.33 Å2
Refinement stepCycle: final / Resolution: 3.8→41.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2342 5 0 2347
Biso mean--111.47 --
Num. residues----109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022627
X-RAY DIFFRACTIONf_angle_d0.8464097
X-RAY DIFFRACTIONf_dihedral_angle_d20.3111305
X-RAY DIFFRACTIONf_chiral_restr0.083545
X-RAY DIFFRACTIONf_plane_restr0.002109
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 (%)
3.8-3.940.3551270.39553155899
3.94-4.090.3839380.340252656499
4.09-4.280.5276200.321250452498
4.28-4.50.466310.335855058198
4.51-4.790.2791130.278551452797
4.79-5.150.326360.261454958599
5.16-5.670.3242280.218352455299
5.67-6.490.2721210.197154056197
6.49-8.170.2683210.194955657796
8.18-41.790.294230.289659061395
Refinement TLS params.Method: refined / Origin x: 11.504 Å / Origin y: -15.607 Å / Origin z: -30.141 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °
Refinement TLS groupSelection details: ( CHAIN X AND RESID 1:109 )

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