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- PDB-6xko: Class III PreQ1 riboswitch mutant A84G -

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Basic information

Entry
Database: PDB / ID: 6xko
TitleClass III PreQ1 riboswitch mutant A84G
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: 2.75 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

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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
Water1629
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)83.798, 83.798, 277.104
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: A84G / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsAdenine 84 mutated to guanine

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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: 4.3 Å3/Da / Density % sol: 71.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 80% 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: 2.75→44.05 Å / Num. obs: 15744 / % possible obs: 99.1 % / Redundancy: 8.7 % / Rpim(I) all: 0.034 / Net I/σ(I): 22.7
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1535 / Rpim(I) all: 0.43 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000v708cdata reduction
HKL-2000v708cdata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4RZD
Resolution: 2.75→44.05 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1569 9.97 %
Rwork0.2081 14175 -
obs0.2097 15744 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.25 Å2 / Biso mean: 85.9 Å2 / Biso min: 35.18 Å2
Refinement stepCycle: final / Resolution: 2.75→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2035 22 9 2066
Biso mean--65.74 57.65 -
Num. residues----95
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062284
X-RAY DIFFRACTIONf_angle_d0.843555
X-RAY DIFFRACTIONf_dihedral_angle_d13.7871137
X-RAY DIFFRACTIONf_chiral_restr0.036474
X-RAY DIFFRACTIONf_plane_restr0.00796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.840.42921400.40611244138499
2.84-2.940.36541410.36851238137999
2.94-3.060.31351460.28251249139599
3.06-3.20.23731290.22841261139099
3.2-3.360.2211410.21641264140599
3.36-3.570.25051410.21531251139299
3.57-3.850.19721430.18161288143199
3.85-4.240.18481390.170112911430100
4.24-4.850.21121390.175313191458100
4.85-6.110.16741490.181613471496100
6.11-44.050.2231610.19681423158498
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1332-0.1031-0.09170.15790.10830.08080.3629-0.7415-0.91720.36730.12880.91740.5646-1.232-0.00030.88180.1914-0.07550.95970.12281.3132-4.318158.3368100.7618
20.1714-0.0835-0.0910.4464-0.0090.1013-0.47760.65880.2054-0.03270.09740.29270.35080.3495-0.00060.72710.1564-0.03840.7311-0.05780.60549.811552.800798.3401
30.285-0.1799-0.02240.12020.04960.16720.47630.7098-0.6611-0.2298-0.17780.24031.0620.79110.00851.01270.227-0.13160.6355-0.05910.846114.784648.0768111.9935
42.2102-0.70562.10110.50370.17384.5543-0.4566-1.1942-0.85951.80490.4986-0.56410.2844-1.08390.19391.19050.24220.04640.753-0.00931.367613.100533.5723110.6092
50.9317-0.3042-0.34280.76980.67490.8167-0.20970.12-0.14-0.60350.25591.08480.2028-0.3113-0.00280.64470.27020.01330.53840.06250.794728.577234.4368103.7958
60.1872-0.2391-0.09760.3190.11530.05320.88390.431.4664-0.73770.00740.58010.01180.12240.00270.99330.04330.10250.69830.10930.814939.971244.428295.6157
70.46460.1299-0.29350.1879-0.05760.4686-0.3705-0.8521-0.50450.91090.18820.1048-0.85931.3723-0.00090.80980.1316-0.15641.00450.12810.870550.907331.992892.1649
80.24240.23020.00370.33230.15970.2127-0.5023-0.8682-0.79080.1150.2554-0.86260.37561.1785-0.00841.0150.1774-0.20011.37480.27121.821667.162825.911490.887
91.43381.25610.70461.24220.3850.69710.17190.14641.47170.58690.2020.41-0.8541-1.58360.01061.1508-0.01380.21080.88020.00070.782536.657439.0231122.5312
100.5794-0.4624-0.3590.56510.10440.38780.3122-0.0685-0.1562-0.43890.1141-0.0531-0.45240.3890.00110.75160.18720.00620.68270.03670.535239.061228.6523107.0918
110.6076-0.0058-0.1190.12730.14050.1710.3197-0.05940.24590.12850.0209-0.17380.08490.65780.00020.86370.065-0.03130.8880.09260.633141.222636.246899.3037
120.11570.0923-0.06580.068-0.05750.2945-0.567-0.40330.6967-0.48940.55970.4424-0.06410.48640.00340.74420.10650.08280.5543-0.00840.683433.054936.5747111.156
130.6017-0.356-0.07960.55050.11580.02340.1934-0.27770.65210.3360.41530.2521-0.48110.138-0.00190.94080.12020.16620.6466-0.09540.739434.93931.7207126.2997
140.6267-0.71120.49740.8069-0.56350.3940.7519-1.63-0.70410.22230.80011.3120.2675-0.00640.02681.43760.13170.1851.48060.36281.074423.730931.0576142.09
150.42050.166-0.07480.16610.11690.22410.3028-1.24130.7133-0.34791.08631.3168-1.0351-1.26090.00211.65480.15930.21812.20680.13151.368330.580929.9275151.2861
160.22720.1225-0.21980.1631-0.28040.4784-0.2396-0.44470.6519-0.6379-0.1847-0.0692-1.4885-2.20310.00271.36630.12590.01641.4983-0.01310.883335.255629.0617144.0676
170.16210.02810.01880.0133-0.00060.00281.19470.9568-1.31660.3238-0.48110.9691-0.01041.03180.00421.1999-0.01050.0450.98290.06081.066224.878531.147131.7613
180.31420.27570.08730.24030.080.07020.3306-0.03150.11870.3195-0.48390.8807-0.22880.61120.00170.8980.22450.04150.77740.10280.910224.169838.8308111.6481
190.8266-0.8761-0.77531.17860.96910.8126-0.26671.3218-0.92740.8563-0.35270.26890.62740.0723-0.01210.91220.3016-0.14930.8356-0.17360.99079.914841.0844103.9107
200.786-0.0315-0.38620.56340.23390.27180.16530.18840.1887-0.28-0.26310.93020.0343-0.3418-0.00021.00980.2378-0.0590.58310.0120.80776.335559.6637105.8743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 67:70)A67 - 70
2X-RAY DIFFRACTION2(chain A and resid 71:74)A71 - 74
3X-RAY DIFFRACTION3(chain A and resid 75:78)A75 - 78
4X-RAY DIFFRACTION4(chain A and resid 79:83)A79 - 83
5X-RAY DIFFRACTION5(chain A and resid 84:87)A84 - 87
6X-RAY DIFFRACTION6(chain A and resid 88:91)A88 - 91
7X-RAY DIFFRACTION7(chain A and resid 92:95)A92 - 95
8X-RAY DIFFRACTION8(chain A and resid 96:101)A96 - 101
9X-RAY DIFFRACTION9(chain A and resid 1:4)A1 - 4
10X-RAY DIFFRACTION10(chain A and resid 5:9)A5 - 9
11X-RAY DIFFRACTION11(chain A and resid 10:14)A10 - 14
12X-RAY DIFFRACTION12(chain A and resid 15:18)A15 - 18
13X-RAY DIFFRACTION13(chain A and resid 19:26)A19 - 26
14X-RAY DIFFRACTION14(chain A and resid 27:30)A27 - 30
15X-RAY DIFFRACTION15(chain A and resid 31:40)A31 - 40
16X-RAY DIFFRACTION16(chain A and resid 41:44)A41 - 44
17X-RAY DIFFRACTION17(chain A and resid 45:49)A45 - 49
18X-RAY DIFFRACTION18(chain A and resid 50:54)A50 - 54
19X-RAY DIFFRACTION19(chain A and resid 55:58)A55 - 58
20X-RAY DIFFRACTION20(chain A and resid 59:66)A59 - 66

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