PDB-6s5b: Non-square conformation of KtrA R16K mutant ring with bound ADP

ID or keywords:

Entry

Database: PDB / ID: 6s5b

Title

Non-square conformation of KtrA R16K mutant ring with bound ADP

Components

Ktr system potassium uptake protein A

Keywords

TRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / non-square conformation octameric ring / adp

Function / homology

Function and homology information

monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.052 Å

Authors

Teixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.

Funding support

Portugal, 2items

Citation

Journal: Elife / Year: 2019
Title: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.

History

Deposition	Jul 1, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6s5b.cif.gz	712.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6s5b.ent.gz	594.6 KB	Display	PDB format
PDBx/mmJSON format	6s5b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6s5b_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6s5b_full_validation.pdf.gz	2.3 MB	Display
Data in XML	6s5b_validation.xml.gz	59.8 KB	Display
Data in CIF	6s5b_validation.cif.gz	76.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/6s5b ftp://data.pdbj.org/pub/pdb/validation_reports/s5/6s5b	HTTPS FTP

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Related structure data

Related structure data	6s2jC 6s5cC 6s5dC 6s5eC 6s5gC 6s5nC 6s5oC 6s7rC 4j90S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6s5g-1 6s5e-1 5bk2-d 5u03-d 4c2b-d 6g2s-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#38 - Feb 2003 Potassium Channels similarity (7)

Deposited unit

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

C: Ktr system potassium uptake protein A

D: Ktr system potassium uptake protein A

E: Ktr system potassium uptake protein A

F: Ktr system potassium uptake protein A

G: Ktr system potassium uptake protein A

H: Ktr system potassium uptake protein A

hetero molecules

203 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

hetero molecules

G: Ktr system potassium uptake protein A

H: Ktr system potassium uptake protein A

hetero molecules

C: Ktr system potassium uptake protein A

D: Ktr system potassium uptake protein A

hetero molecules

E: Ktr system potassium uptake protein A

F: Ktr system potassium uptake protein A

hetero molecules

defined by author&software
Evidence: gel filtration
203 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.818, 137.429, 202.617
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ktr system potassium uptake protein A / K(+)-uptake protein KtrA Mass: 24888.746 Da / Num. of mol.: 8 / Mutation: R16K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3	59.01
2

Crystal grow

Temperature (K)	Crystal-ID	Method	Details
293.15	1	vapor diffusion	100mM HEPES-NaOH pH 7.5, 6% PEG 8000, 20% ethylene glycol
293.15	2	vapor diffusion	100mM HEPES-NaOH pH 7.5, 8% PEG 8000, 20% ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97948 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97948 Å / Relative weight: 1
Reflection	Resolution: 3.05→49.51 Å / Num. obs: 46032 / % possible obs: 99.2 % / Redundancy: 8.3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.148 / R_pim(I) all: 0.054 / R_rim(I) all: 0.158 / Net I/σ(I): 15.9
Reflection shell	Resolution: 3.05→3.16 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.474 / Num. unique obs: 4076 / CC_1/2: 0.886 / R_pim(I) all: 0.249 / R_rim(I) all: 0.538 / % possible all: 91.6

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4j90

4j90

Resolution: 3.052→48.168 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.4 / Phase error: 27.86

	R_factor	Num. reflection	% reflection
R_free	0.2429	4283	5.03 %
R_work	0.2093	-	-
obs	0.211	46032	96.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.052→48.168 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13568	0	216	0	13784

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	14008
X-RAY DIFFRACTION	f_angle_d	0.76	18960
X-RAY DIFFRACTION	f_dihedral_angle_d	13.479	5232
X-RAY DIFFRACTION	f_chiral_restr	0.029	2200
X-RAY DIFFRACTION	f_plane_restr	0.002	2376

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0519-3.0866	0.5333	108	0.4272	1722	X-RAY DIFFRACTION	63
3.0866-3.1229	0.4152	129	0.4214	2497	X-RAY DIFFRACTION	89
3.1229-3.1609	0.447	158	0.3806	2431	X-RAY DIFFRACTION	89
3.1609-3.2009	0.3976	143	0.362	2542	X-RAY DIFFRACTION	91
3.2009-3.2431	0.4084	171	0.3559	2639	X-RAY DIFFRACTION	96
3.2431-3.2875	0.3855	145	0.3242	2651	X-RAY DIFFRACTION	95
3.2875-3.3344	0.3705	152	0.3086	2661	X-RAY DIFFRACTION	97
3.3344-3.3842	0.3191	129	0.2815	2762	X-RAY DIFFRACTION	98
3.3842-3.4371	0.2984	154	0.2735	2752	X-RAY DIFFRACTION	98
3.4371-3.4934	0.2744	184	0.2517	2662	X-RAY DIFFRACTION	98
3.4934-3.5536	0.3044	141	0.2443	2782	X-RAY DIFFRACTION	98
3.5536-3.6182	0.2847	127	0.2565	2715	X-RAY DIFFRACTION	99
3.6182-3.6878	0.3175	151	0.2542	2758	X-RAY DIFFRACTION	98
3.6878-3.763	0.2826	120	0.2665	2799	X-RAY DIFFRACTION	99
3.763-3.8448	0.2709	146	0.2479	2745	X-RAY DIFFRACTION	99
3.8448-3.9342	0.2472	132	0.2239	2816	X-RAY DIFFRACTION	99
3.9342-4.0325	0.212	133	0.21	2765	X-RAY DIFFRACTION	100
4.0325-4.1415	0.3016	152	0.199	2779	X-RAY DIFFRACTION	100
4.1415-4.2633	0.2401	163	0.1907	2755	X-RAY DIFFRACTION	100
4.2633-4.4008	0.2307	124	0.1833	2804	X-RAY DIFFRACTION	99
4.4008-4.558	0.2276	157	0.1669	2780	X-RAY DIFFRACTION	100
4.558-4.7404	0.2368	148	0.1746	2771	X-RAY DIFFRACTION	100
4.7404-4.9559	0.2313	117	0.1761	2782	X-RAY DIFFRACTION	100
4.9559-5.2169	0.2143	186	0.1774	2764	X-RAY DIFFRACTION	100
5.2169-5.5433	0.2007	134	0.1731	2796	X-RAY DIFFRACTION	100
5.5433-5.9706	0.214	143	0.1903	2792	X-RAY DIFFRACTION	100
5.9706-6.5701	0.2175	131	0.2004	2796	X-RAY DIFFRACTION	100
6.5701-7.5177	0.1953	127	0.2056	2786	X-RAY DIFFRACTION	100
7.5177-9.4597	0.1663	132	0.1597	2810	X-RAY DIFFRACTION	100
9.4597-48.1735	0.1871	146	0.1799	2741	X-RAY DIFFRACTION	99

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	8.1403	-1.0712	-2.7886	8.0505	-1.9913	10.4542	0.2977	0.823	-0.2995	-0.7452	-0.3415	-1.1473	2.0658	1.7188	0.0144	0.9369	0.445	0.005	1.2296	0.0182	0.7303	-11.3031	-19.2706	-7.2204
2	4.0125	3.2995	3.8968	1.7656	1.6876	7.5148	-0.0933	0.0091	0.7362	-0.0605	-0.0523	0.8212	-0.6884	-1.1919	-0.0994	0.7171	0.204	0.1118	0.8499	0.2023	0.9076	-20.6885	-7.3778	3.7778
3	8.1078	3.0904	1.9961	3.4219	0.2038	3.9224	0.7687	-1.171	0.2174	1.1984	-0.5402	0.425	-0.7081	0.0996	-0.163	1.0524	-0.0717	0.1371	0.9709	-0.1618	0.7865	-25.1329	-17.8301	31.2552
4	9.7221	0.7116	0.0596	6.7266	-0.3613	6.5548	0.2457	0.4572	0.9676	0.0802	-0.2835	1.0392	-0.6977	-0.4326	0.0587	0.5402	0.0055	-0.0348	0.6139	0.0722	0.7401	-7.958	4.0309	16.6563
5	7.5476	6.1311	6.8755	5.8218	2.0309	8.7065	0.0656	0.2239	-0.8856	0.1576	-0.3269	0.2467	0.8354	1.3046	0.161	0.5188	0.2009	0.0737	0.8859	0.1903	0.9827	-5.8973	-14.311	12.7124
6	8.1207	4.5743	-2.7753	8.3454	4.2098	9.2051	-0.562	-0.1747	-0.1661	-0.5942	0.1894	0.5873	0.4875	-0.05	0.3201	0.7883	0.0876	-0.0773	0.6213	0.1374	0.7824	-31.839	-29.4508	13.8377
7	5.3972	-0.1688	0.4554	5.7901	2.0548	8.6347	0.1722	-0.2303	-0.0632	0.9388	-0.3508	0.921	1.5531	-2.1566	0.1559	0.8075	-0.3008	-0.0169	1.0506	-0.0333	0.8335	-27.2735	-9.615	77.0741
8	3.2888	-1.1772	-2.9859	1.8804	-2.6801	7.6227	-0.1059	-0.4604	0.9078	0.3067	0.1026	-1.1624	-0.7906	0.9174	-0.102	0.6179	-0.1231	-0.0646	0.8196	-0.3347	1.2839	-14.2568	2.1197	70.8282
9	8.0041	-1.2307	-2.8149	7.1052	-2.8738	4.6616	0.2765	0.8664	0.6097	-0.5101	0.2882	-1.7484	-0.3221	0.6902	-0.5824	0.6389	-0.09	0.0269	0.9043	-0.0655	1.1883	1.4535	-10.1932	47.9977
10	5.0211	-1.0192	4.5105	7.2878	-1.9461	7.8687	-0.5709	0.2919	2.9827	0.2372	-0.222	-1.4879	-1.5693	0.6316	0.7359	0.7539	-0.0385	-0.0287	0.6615	0.0461	1.6062	-19.5463	13.3135	53.4829
11	6.6604	-5.3369	6.1091	7.1325	-3.1368	6.0584	0.0843	0.7555	0.3276	-0.1918	-0.4575	-0.8012	0.0505	0.4255	0.3891	0.3966	-0.0748	0.0511	0.6647	-0.0266	0.7394	-22.8654	-3.168	54.4734
12	5.9373	-2.3808	-5.2446	8.1498	-1.0438	7.5549	-0.691	-1.9382	0.1772	1.1091	0.8302	-1.3163	0.8624	1.3711	-0.1776	0.9683	0.2291	-0.3752	1.0364	-0.217	0.9965	0.8012	-19.5597	67.754
13	9.5442	-0.8561	-0.7234	7.4665	2.913	6.6993	0.2574	0.7143	0.4444	-0.6846	-0.1018	0.8056	-0.907	-0.923	-0.219	0.6386	0.115	-0.0677	0.6256	0.1732	0.6156	-32.0562	-51.7157	31.5547
14	4.4011	2.3305	-3.4371	1.3819	-2.3492	2.6616	-0.0527	-0.1437	-0.4391	0.2223	0.0709	-0.8214	1.2119	0.972	0.0607	0.8086	0.1544	-0.1864	0.5474	-0.0444	0.8426	-22.248	-63.5608	42.1525
15	7.4808	1.996	-2.2899	9.0604	-0.1742	3.6692	0.8487	-1.6555	-0.2435	1.5344	-0.5561	-0.578	1.39	0.2908	-0.3865	1.2586	-0.2185	-0.4834	1.0541	0.0491	1.007	-17.7194	-53.6332	69.5351
16	5.8246	2.0053	0.5655	10.7732	0.2904	5.1018	0.1743	-0.7156	-1.257	1.1284	-0.3163	-1.4691	0.7046	0.27	0.1544	0.698	-0.1162	-0.1186	0.5793	0.1277	0.7851	-35.0616	-75.2748	54.7843
17	9.39	7.2776	-4.8194	5.2705	-1.9558	6.2188	0.2775	-0.7174	0.808	0.4285	-0.4614	-0.2536	-0.3369	0.1535	0.2795	0.5431	0.067	-0.0798	0.4816	0.0133	0.7414	-36.9819	-56.7992	51.4351
18	2.8525	3.3587	-0.4884	7.4504	-2.8416	6.0198	-0.0517	0.1261	-0.279	-0.1898	0.1087	-1.0887	0.0151	0.868	0.0101	0.5913	-0.0471	-0.0804	0.755	-0.1659	0.9436	-11.3223	-41.9089	52.3648
19	9.9191	-0.4925	3.4092	7.8258	3.4329	3.6033	-0.475	-0.4064	0.302	-0.5546	-0.2829	1.2016	-1.8078	-1.6491	0.7261	0.8617	0.3373	-0.1011	1.0026	-0.0393	0.7217	-71.742	13.5318	-9.769
20	4.4166	4.4713	0.0209	10.0381	5.8934	9.6783	-0.1993	0.8973	-0.5009	-0.7133	0.3251	-0.1373	-0.6381	0.2929	-0.1023	0.548	0.0897	-0.0126	0.7973	0.0824	0.5547	-63.1027	3.7986	-17.2631
21	6.9995	-3.263	8.7894	8.1477	-8.8599	2.2049	-0.8015	-1.6432	-1.2308	0.2535	0.5368	-0.8754	-0.2718	0.9529	0.1647	0.6617	0.2646	-0.1357	1.0643	0.2428	1.246	-54.8217	-2.3603	4.0327
22	5.8866	2.7477	0.6767	4.522	-4.5315	8.1847	0.0171	-1.3913	0.3586	0.7703	0.0379	-0.5741	-0.7595	0.1024	0.0102	0.7405	0.1467	-0.0127	1.3484	-0.0142	0.8639	-41.0744	7.7909	16.2002
23	6.9894	1.952	-5.1222	8.0928	1.8651	6.0563	-0.2935	-0.7342	-1.9627	0.2709	-0.1872	-0.7329	0.8309	0.6852	0.377	0.6004	0.1614	-0.0646	1.0518	0.3839	1.0814	-62.6793	-13.726	9.3638
24	9.4446	8.0582	-7.6809	6.6631	-5.3811	7.9998	-0.0881	-0.5873	0.1777	0.2596	0.1137	0.3514	-0.447	-0.0142	-0.0745	0.5436	0.1544	-0.0218	0.7771	0.0205	0.7115	-65.6876	4.6408	6.919
25	8.8098	0.9612	3.0953	6.905	-0.6881	8.7322	-0.5092	1.0169	0.6352	-0.4751	0.3616	-0.3788	-0.873	0.5347	0.1939	0.7408	-0.1104	0.1071	0.8864	0.1143	0.7156	-40.3887	18.2111	-2.7168

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 106 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 107 through 137 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 138 through 222 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 7 through 106 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 107 through 137 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 138 through 222 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 7 through 106 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 107 through 137 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 138 through 222 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 7 through 94 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 95 through 137 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 138 through 222 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 7 through 106 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 107 through 137 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 138 through 222 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 7 through 106 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 107 through 137 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 138 through 222 )
19	X-RAY DIFFRACTION	19	chain 'G' and (resid 7 through 66 )
20	X-RAY DIFFRACTION	20	chain 'G' and (resid 67 through 123 )
21	X-RAY DIFFRACTION	21	chain 'G' and (resid 124 through 137 )
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 138 through 222 )
23	X-RAY DIFFRACTION	23	chain 'H' and (resid 7 through 106 )
24	X-RAY DIFFRACTION	24	chain 'H' and (resid 107 through 137 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 138 through 222 )

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Yorodumi