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- PDB-6xkn: Class III PreQ1 riboswitch mutant A52G -

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Basic information

Entry
Database: PDB / ID: 6xkn
TitleClass III PreQ1 riboswitch mutant A52G
ComponentsClass III PreQ1 riboswitch
KeywordsRNA / PREQ1 / QUEUOSINE / THREE-WAY HELICAL JUNCTION / APTAMER / METABOLITE / TRANSLATIONAL REGULATION / HL(OUT)-TYPE PSEUDOKNOT / RIBOSWITCH
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesFaecalibacterium prausnitzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.73 Å
AuthorsSrivastava, K.Y. / Jenkins, J.L. / Wedekind, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM63162-14 United States
CitationJournal: To Be Published
Title: New insights into Class III PreQ1 metabolite binding
Authors: Srivastava, K.Y. / Jenkins, J.L. / Wedekind, J.E.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Jun 19, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conn / struct_site / struct_site_gen
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _entity.pdbx_number_of_molecules / _pdbx_entry_details.has_ligand_of_interest / _pdbx_validate_close_contact.dist / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _software.classification / _software.name / _software.version
Description: Model orientation/position
Details: We conducted a structural and functional analysis of the riboswitch and noticed that one of the bases (C83) was modeled in a highly unlikely syn conformation. We chose to correct this ...Details: We conducted a structural and functional analysis of the riboswitch and noticed that one of the bases (C83) was modeled in a highly unlikely syn conformation. We chose to correct this conformation using the same dataset already deposited in the PDB. We refined the structure with the new anti-conformation and took the opportunity to improve the geometry and clash score.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class III PreQ1 riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8342
Polymers32,6551
Non-polymers1791
Water1267
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)80.137, 80.137, 281.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain Class III PreQ1 riboswitch


Mass: 32655.254 Da / Num. of mol.: 1 / Mutation: A52G / Source method: obtained synthetically / Source: (synth.) Faecalibacterium prausnitzii (bacteria)
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.99 Å3/Da / Density % sol: 69.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 85% Tacsimate pH 7.0, 10 mM magnesium acetate, 6 mM cobalt haxammine, 1 mM spermine
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6279 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6279 Å / Relative weight: 1
ReflectionResolution: 2.73→24.71 Å / Num. obs: 15078 / % possible obs: 97.3 % / Redundancy: 8.4 % / Rpim(I) all: 0.035 / Net I/σ(I): 20
Reflection shellResolution: 2.73→2.83 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1473 / Rpim(I) all: 0.357 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v708cdata reduction
HKL-2000v708cdata scaling
PDB_EXTRACT3.25data extraction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4RZD

4rzd


Resolution: 2.73→24.71 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1467 9.98 %
Rwork0.2357 --
obs0.2368 14702 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.13 Å2
Refinement stepCycle: LAST / Resolution: 2.73→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2055 13 7 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012306
X-RAY DIFFRACTIONf_angle_d0.4683589
X-RAY DIFFRACTIONf_dihedral_angle_d13.6281159
X-RAY DIFFRACTIONf_chiral_restr0.022479
X-RAY DIFFRACTIONf_plane_restr0.00298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.830.41221560.43341280X-RAY DIFFRACTION98
2.83-2.940.43241400.41091293X-RAY DIFFRACTION98
2.94-3.070.30391360.33331293X-RAY DIFFRACTION97
3.07-3.230.2851430.27951245X-RAY DIFFRACTION94
3.23-3.440.26571350.28971278X-RAY DIFFRACTION96
3.44-3.70.28891530.26321273X-RAY DIFFRACTION95
3.7-4.070.21721390.21811334X-RAY DIFFRACTION97
4.07-4.660.211430.18951355X-RAY DIFFRACTION99
4.66-5.850.22411550.19541392X-RAY DIFFRACTION99
5.85-24.710.21191670.19651492X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.0632-0.32512.83242.6221-1.17855.82450.19680.01330.3256-0.04070.1359-0.0548-0.44770.2117-0.12661.14980.08850.04590.7270.06040.37233.98531.5316115.0622
21.72860.55243.32821.5089-0.38587.8869-0.1190.00040.4722-0.05590.67830.2759-0.11630.6318-0.26241.06050.14430.06431.0206-0.05240.380533.468631.2465111.5749
39.1029-1.2745-2.3236.3492-4.25725.12750.9377-1.383-0.03770.68071.15021.1883-0.0009-1.3042-1.90691.2643-0.05050.04411.4450.07220.611825.277631.5537140.458
45.21454.68823.32134.5242.54672.66051.06580.5438-1.80592.12350.9973-1.4175-0.4070.1067-2.12082.00940.1325-0.08682.0347-0.04191.024528.504322.6563155.1274
57.29691.66943.68563.0819-2.46495.9184-1.0757-1.26881.14280.77391.52380.72280.2117-1.0884-0.61011.3130.1833-0.02572.0785-0.10590.894427.858927.8882146.6809
63.71731.6189-3.04495.5061-3.46739.15151.231-0.0267-0.51270.7737-0.19510.81380.2958-0.2178-0.62241.42620.1743-0.00671.33510.0390.574821.545533.7719129.2637
72.493-0.8324-0.31848.95331.38211.27210.7172-0.8357-1.0961-0.1212-0.93020.3424-0.27280.05720.41411.29470.2196-0.02891.20340.02330.411516.952734.8619109.8776
81.6943-0.88980.92520.9222-0.58993.0703-0.18760.25840.267-0.9793-0.01440.5408-0.5803-0.64980.13240.97350.1125-0.02310.5804-0.02440.44566.330548.4296109.5258
94.46390.96675.15663.28111.64488.1725-1.0678-0.3690.90930.18350.44490.7709-1.196-0.45690.53141.10970.224-0.09570.7724-0.01610.6223-0.841954.9297101.0562
109.11780.10690.84682.5058-3.116.9588-0.11540.1929-1.29770.90620.41750.18470.21531.12060.09211.14780.3824-0.0590.7615-0.17240.057312.48743.943112.5179
113.0737-0.39050.68247.8651.85967.80030.0864-0.7538-0.19961.93921.1061-0.20240.8309-0.7609-0.95691.33820.27460.19260.84330.31491.25999.947229.11111.7183
128.92520.8659-6.44941.7338-1.13765.70640.83220.27660.82430.2606-0.25190.4725-1.29790.4995-0.47251.18910.0649-0.0141.09380.05760.400734.067435.019499.005
137.8299-3.062.322.7855-0.37810.9345-1.4825-0.6450.58660.71780.42-1.3519-0.05853.32210.86081.108-0.034-0.17011.98950.30931.109161.165621.898493.8485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 33 )
5X-RAY DIFFRACTION5chain 'A' and (resid 39 through 46 )
6X-RAY DIFFRACTION6chain 'A' and (resid 47 through 51 )
7X-RAY DIFFRACTION7chain 'A' and (resid 52 through 56 )
8X-RAY DIFFRACTION8chain 'A' and (resid 57 through 63 )
9X-RAY DIFFRACTION9chain 'A' and (resid 64 through 72 )
10X-RAY DIFFRACTION10chain 'A' and (resid 73 through 79 )
11X-RAY DIFFRACTION11chain 'A' and (resid 80 through 83 )
12X-RAY DIFFRACTION12chain 'A' and (resid 84 through 94 )
13X-RAY DIFFRACTION13chain 'A' and (resid 95 through 101 )

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