PDB-6xko: Class III PreQ1 riboswitch mutant A84G

ID or keywords:

Entry

Database: PDB / ID: 6xko

Title

Class III PreQ1 riboswitch mutant A84G

Components

Class III PreQ1 riboswitch

Keywords

RNA / PREQ1 / QUEUOSINE / THREE-WAY HELICAL JUNCTION / APTAMER / METABOLITE / TRANSLATIONAL REGULATION / HL(OUT)-TYPE PSEUDOKNOT / RIBOSWITCH

Function / homology

7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Faecalibacterium prausnitzii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.75 Å

Authors

Srivastava, K.Y. / Jenkins, J.L. / Wedekind, J.E.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2024
Title: Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.
Authors: Srivastava, Y. / Akinyemi, O. / Rohe, T.C. / Pritchett, E.M. / Baker, C.D. / Sharma, A. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.

History

Deposition	Jun 26, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Dec 11, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6xko.cif.gz	140.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6xko.ent.gz	114.4 KB	Display	PDB format
PDBx/mmJSON format	6xko.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6xko_validation.pdf.gz	414.4 KB	Display	wwPDB validaton report
Full document	6xko_full_validation.pdf.gz	414.4 KB	Display
Data in XML	6xko_validation.xml.gz	4.7 KB	Display
Data in CIF	6xko_validation.cif.gz	6.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xk/6xko ftp://data.pdbj.org/pub/pdb/validation_reports/xk/6xko	HTTPS FTP

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Related structure data

Related structure data	6xknC 8tozC 8vpvC 4rzdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6xkn-d 4rzd-d 5gw1-3 5gw0-1 6rj0-d 4xco-2 3fk3-d 6axj-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (3) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (3)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#15 - Mar 2001
Transfer RNA
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#245 - May 2020
Spliceosomes
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Class III PreQ1 riboswitch

hetero molecules

32.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: isothermal titration calorimetry

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 number	179
Space group name H-M	P6₅22

#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 interest	N
Has protein modification	N
Sequence details	Adenine 84 mutated to guanine

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.3 Å³/Da / Density % sol: 71.4 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6279 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6279 Å / Relative weight: 1
Reflection	Resolution: 2.75→44.05 Å / Num. obs: 15744 / % possible obs: 99.1 % / Redundancy: 8.7 % / R_pim(I) all: 0.034 / Net I/σ(I): 22.7
Reflection shell	Resolution: 2.75→2.85 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1535 / R_pim(I) all: 0.43 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000	v708c	data reduction
HKL-2000	v708c	data scaling
PHENIX	1.17.1_3660	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4RZD

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

	R_factor	Num. reflection	% reflection
R_free	0.2233	1569	9.97 %
R_work	0.2081	14175	-
obs	0.2097	15744	99.13 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 191.25 Å² / B_iso mean: 85.9 Å² / B_iso min: 35.18 Å²

Refinement step

Cycle: final / Resolution: 2.75→44.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	2035	22	9	2066
B_iso mean	-	-	65.74	57.65	-
Num. residues	-	-	-	-	95

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2284
X-RAY DIFFRACTION	f_angle_d	0.84	3555
X-RAY DIFFRACTION	f_dihedral_angle_d	13.787	1137
X-RAY DIFFRACTION	f_chiral_restr	0.036	474
X-RAY DIFFRACTION	f_plane_restr	0.007	96

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.75-2.84	0.4292	140	0.4061	1244	1384	99
2.84-2.94	0.3654	141	0.3685	1238	1379	99
2.94-3.06	0.3135	146	0.2825	1249	1395	99
3.06-3.2	0.2373	129	0.2284	1261	1390	99
3.2-3.36	0.221	141	0.2164	1264	1405	99
3.36-3.57	0.2505	141	0.2153	1251	1392	99
3.57-3.85	0.1972	143	0.1816	1288	1431	99
3.85-4.24	0.1848	139	0.1701	1291	1430	100
4.24-4.85	0.2112	139	0.1753	1319	1458	100
4.85-6.11	0.1674	149	0.1816	1347	1496	100
6.11-44.05	0.223	161	0.1968	1423	1584	98

Refinement TLS params.

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

ID	L11 (°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)
1	0.1332	-0.1031	-0.0917	0.1579	0.1083	0.0808	0.3629	-0.7415	-0.9172	0.3673	0.1288	0.9174	0.5646	-1.232	-0.0003	0.8818	0.1914	-0.0755	0.9597	0.1228	1.3132	-4.3181	58.3368	100.7618
2	0.1714	-0.0835	-0.091	0.4464	-0.009	0.1013	-0.4776	0.6588	0.2054	-0.0327	0.0974	0.2927	0.3508	0.3495	-0.0006	0.7271	0.1564	-0.0384	0.7311	-0.0578	0.6054	9.8115	52.8007	98.3401
3	0.285	-0.1799	-0.0224	0.1202	0.0496	0.1672	0.4763	0.7098	-0.6611	-0.2298	-0.1778	0.2403	1.062	0.7911	0.0085	1.0127	0.227	-0.1316	0.6355	-0.0591	0.8461	14.7846	48.0768	111.9935
4	2.2102	-0.7056	2.1011	0.5037	0.1738	4.5543	-0.4566	-1.1942	-0.8595	1.8049	0.4986	-0.5641	0.2844	-1.0839	0.1939	1.1905	0.2422	0.0464	0.753	-0.0093	1.3676	13.1005	33.5723	110.6092
5	0.9317	-0.3042	-0.3428	0.7698	0.6749	0.8167	-0.2097	0.12	-0.14	-0.6035	0.2559	1.0848	0.2028	-0.3113	-0.0028	0.6447	0.2702	0.0133	0.5384	0.0625	0.7947	28.5772	34.4368	103.7958
6	0.1872	-0.2391	-0.0976	0.319	0.1153	0.0532	0.8839	0.43	1.4664	-0.7377	0.0074	0.5801	0.0118	0.1224	0.0027	0.9933	0.0433	0.1025	0.6983	0.1093	0.8149	39.9712	44.4282	95.6157
7	0.4646	0.1299	-0.2935	0.1879	-0.0576	0.4686	-0.3705	-0.8521	-0.5045	0.9109	0.1882	0.1048	-0.8593	1.3723	-0.0009	0.8098	0.1316	-0.1564	1.0045	0.1281	0.8705	50.9073	31.9928	92.1649
8	0.2424	0.2302	0.0037	0.3323	0.1597	0.2127	-0.5023	-0.8682	-0.7908	0.115	0.2554	-0.8626	0.3756	1.1785	-0.0084	1.015	0.1774	-0.2001	1.3748	0.2712	1.8216	67.1628	25.9114	90.887
9	1.4338	1.2561	0.7046	1.2422	0.385	0.6971	0.1719	0.1464	1.4717	0.5869	0.202	0.41	-0.8541	-1.5836	0.0106	1.1508	-0.0138	0.2108	0.8802	0.0007	0.7825	36.6574	39.0231	122.5312
10	0.5794	-0.4624	-0.359	0.5651	0.1044	0.3878	0.3122	-0.0685	-0.1562	-0.4389	0.1141	-0.0531	-0.4524	0.389	0.0011	0.7516	0.1872	0.0062	0.6827	0.0367	0.5352	39.0612	28.6523	107.0918
11	0.6076	-0.0058	-0.119	0.1273	0.1405	0.171	0.3197	-0.0594	0.2459	0.1285	0.0209	-0.1738	0.0849	0.6578	0.0002	0.8637	0.065	-0.0313	0.888	0.0926	0.6331	41.2226	36.2468	99.3037
12	0.1157	0.0923	-0.0658	0.068	-0.0575	0.2945	-0.567	-0.4033	0.6967	-0.4894	0.5597	0.4424	-0.0641	0.4864	0.0034	0.7442	0.1065	0.0828	0.5543	-0.0084	0.6834	33.0549	36.5747	111.156
13	0.6017	-0.356	-0.0796	0.5505	0.1158	0.0234	0.1934	-0.2777	0.6521	0.336	0.4153	0.2521	-0.4811	0.138	-0.0019	0.9408	0.1202	0.1662	0.6466	-0.0954	0.7394	34.939	31.7207	126.2997
14	0.6267	-0.7112	0.4974	0.8069	-0.5635	0.394	0.7519	-1.63	-0.7041	0.2223	0.8001	1.312	0.2675	-0.0064	0.0268	1.4376	0.1317	0.185	1.4806	0.3628	1.0744	23.7309	31.0576	142.09
15	0.4205	0.166	-0.0748	0.1661	0.1169	0.2241	0.3028	-1.2413	0.7133	-0.3479	1.0863	1.3168	-1.0351	-1.2609	0.0021	1.6548	0.1593	0.2181	2.2068	0.1315	1.3683	30.5809	29.9275	151.2861
16	0.2272	0.1225	-0.2198	0.1631	-0.2804	0.4784	-0.2396	-0.4447	0.6519	-0.6379	-0.1847	-0.0692	-1.4885	-2.2031	0.0027	1.3663	0.1259	0.0164	1.4983	-0.0131	0.8833	35.2556	29.0617	144.0676
17	0.1621	0.0281	0.0188	0.0133	-0.0006	0.0028	1.1947	0.9568	-1.3166	0.3238	-0.4811	0.9691	-0.0104	1.0318	0.0042	1.1999	-0.0105	0.045	0.9829	0.0608	1.0662	24.8785	31.147	131.7613
18	0.3142	0.2757	0.0873	0.2403	0.08	0.0702	0.3306	-0.0315	0.1187	0.3195	-0.4839	0.8807	-0.2288	0.6112	0.0017	0.898	0.2245	0.0415	0.7774	0.1028	0.9102	24.1698	38.8308	111.6481
19	0.8266	-0.8761	-0.7753	1.1786	0.9691	0.8126	-0.2667	1.3218	-0.9274	0.8563	-0.3527	0.2689	0.6274	0.0723	-0.0121	0.9122	0.3016	-0.1493	0.8356	-0.1736	0.9907	9.9148	41.0844	103.9107
20	0.786	-0.0315	-0.3862	0.5634	0.2339	0.2718	0.1653	0.1884	0.1887	-0.28	-0.2631	0.9302	0.0343	-0.3418	-0.0002	1.0098	0.2378	-0.059	0.5831	0.012	0.8077	6.3355	59.6637	105.8743

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 67:70)	A	67 - 70
2	X-RAY DIFFRACTION	2	(chain A and resid 71:74)	A	71 - 74
3	X-RAY DIFFRACTION	3	(chain A and resid 75:78)	A	75 - 78
4	X-RAY DIFFRACTION	4	(chain A and resid 79:83)	A	79 - 83
5	X-RAY DIFFRACTION	5	(chain A and resid 84:87)	A	84 - 87
6	X-RAY DIFFRACTION	6	(chain A and resid 88:91)	A	88 - 91
7	X-RAY DIFFRACTION	7	(chain A and resid 92:95)	A	92 - 95
8	X-RAY DIFFRACTION	8	(chain A and resid 96:101)	A	96 - 101
9	X-RAY DIFFRACTION	9	(chain A and resid 1:4)	A	1 - 4
10	X-RAY DIFFRACTION	10	(chain A and resid 5:9)	A	5 - 9
11	X-RAY DIFFRACTION	11	(chain A and resid 10:14)	A	10 - 14
12	X-RAY DIFFRACTION	12	(chain A and resid 15:18)	A	15 - 18
13	X-RAY DIFFRACTION	13	(chain A and resid 19:26)	A	19 - 26
14	X-RAY DIFFRACTION	14	(chain A and resid 27:30)	A	27 - 30
15	X-RAY DIFFRACTION	15	(chain A and resid 31:40)	A	31 - 40
16	X-RAY DIFFRACTION	16	(chain A and resid 41:44)	A	41 - 44
17	X-RAY DIFFRACTION	17	(chain A and resid 45:49)	A	45 - 49
18	X-RAY DIFFRACTION	18	(chain A and resid 50:54)	A	50 - 54
19	X-RAY DIFFRACTION	19	(chain A and resid 55:58)	A	55 - 58
20	X-RAY DIFFRACTION	20	(chain A and resid 59:66)	A	59 - 66

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