PDB-6s2j: Square conformation of KtrA R16K mutant ring with bound ATP

Basic information

• Entry: Database: PDB / ID: 6s2j
• Title: Square conformation of KtrA R16K mutant ring with bound ATP
• Components: Ktr system potassium uptake protein A
• Keywords: TRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / magnesium / square conformation octameric ring / atp

Function / homology

Function:

monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane

Domain/homology:

Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ADENOSINE-5'-TRIPHOSPHATE / Ktr system potassium uptake protein A

• Biological species: Bacillus subtilis (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
• Authors: Teixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.

Funding support

Portugal, 2items

Organization	Grant number	Country
Fundacao para a Ciencia e a Tecnologia	PTDC/BIA-BQM/29863/2017	Portugal
Fundacao para a Ciencia e a Tecnologia	POCI-01-0145-FEDER-007274	Portugal

• 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	Jun 21, 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 / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Assembly

Deposited unit

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

hetero molecules

Summary:

• 50.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,816	5
Polymers	49,777	2
Non-polymers	1,039	3
Water	36	2

1

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

hetero molecules

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

hetero molecules

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

hetero molecules

A: Ktr system potassium uptake protein A

B: Ktr system potassium uptake protein A

hetero molecules

Summary:

• defined by author
• Evidence: gel filtration
• 203 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	203,265	20
Polymers	199,110	8
Non-polymers	4,155	12
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_655	-y+1,x,z	1
crystal symmetry operation	2_665	-x+1,-y+1,z	1
crystal symmetry operation	4_565	y,-x+1,z	1

Unit cell

Length a, b, c (Å)	123.276, 123.276, 84.451
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Components

#1: Protein

A B Ktr system potassium uptake protein A / K(+)-uptake protein KtrA

Details:

Mass: 24888.746 Da / Num. of mol.: 2 / Mutation: R16K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080

#2: Chemical

A-601 A-602 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate

Details:

Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

#3: Chemical

A-603 ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.21 ų/Da / Density % sol: 61.69 %
• Crystal grow: Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris-HCl pH 8.5; 8% polyethylene glycol 8000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95424 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.95424 Å / Relative weight: 1
• Reflection: Resolution: 2.67→46.165 Å / Num. obs: 17872 / % possible obs: 99 % / Redundancy: 4.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.028 / R_rim(I) all: 0.062 / Net I/σ(I): 13.9
• Reflection shell: Resolution: 2.67→2.8 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.868 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2313 / CC_1/2: 0.541 / R_pim(I) all: 0.449 / R_rim(I) all: 0.981 / % possible all: 96.5

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: 2.67→46.165 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0.73 / Phase error: 29.47

	Rfactor	Num. reflection	% reflection
Rfree	0.2357	3506	10.16 %
Rwork	0.1896	-	-
obs	0.1942	17870	97.63 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.67→46.165 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3408	0	63	2	3473

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	3532
X-RAY DIFFRACTION	f_angle_d	1.086	4791
X-RAY DIFFRACTION	f_dihedral_angle_d	14.891	1318
X-RAY DIFFRACTION	f_chiral_restr	0.042	552
X-RAY DIFFRACTION	f_plane_restr	0.004	598

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.6698-2.7063	0.4121	140	0.3897	1073	X-RAY DIFFRACTION	85
2.7063-2.745	0.3648	164	0.3807	1209	X-RAY DIFFRACTION	98
2.745-2.786	0.405	132	0.3534	1267	X-RAY DIFFRACTION	98
2.786-2.8295	0.3618	140	0.3477	1232	X-RAY DIFFRACTION	98
2.8295-2.8759	0.466	165	0.3347	1235	X-RAY DIFFRACTION	99
2.8759-2.9255	0.3911	155	0.3162	1265	X-RAY DIFFRACTION	98
2.9255-2.9787	0.2458	119	0.2951	1218	X-RAY DIFFRACTION	99
2.9787-3.0359	0.3479	105	0.2632	1310	X-RAY DIFFRACTION	98
3.0359-3.0979	0.3	196	0.2575	1208	X-RAY DIFFRACTION	98
3.0979-3.1652	0.3652	130	0.2535	1244	X-RAY DIFFRACTION	99
3.1652-3.2388	0.367	146	0.276	1264	X-RAY DIFFRACTION	98
3.2388-3.3198	0.2619	121	0.266	1291	X-RAY DIFFRACTION	99
3.3198-3.4096	0.3419	136	0.241	1223	X-RAY DIFFRACTION	98
3.4096-3.5099	0.3373	140	0.2077	1252	X-RAY DIFFRACTION	98
3.5099-3.6231	0.2689	144	0.2072	1259	X-RAY DIFFRACTION	99
3.6231-3.7525	0.228	118	0.1963	1253	X-RAY DIFFRACTION	98
3.7525-3.9027	0.2414	149	0.1974	1233	X-RAY DIFFRACTION	97
3.9027-4.0802	0.2399	152	0.1815	1234	X-RAY DIFFRACTION	98
4.0802-4.2952	0.2472	113	0.1756	1238	X-RAY DIFFRACTION	97
4.2952-4.5641	0.1856	125	0.1464	1282	X-RAY DIFFRACTION	99
4.5641-4.9161	0.1947	120	0.131	1261	X-RAY DIFFRACTION	98
4.9161-5.4102	0.1756	171	0.1546	1219	X-RAY DIFFRACTION	97
5.4102-6.1914	0.2285	148	0.1792	1218	X-RAY DIFFRACTION	97
6.1914-7.7944	0.1976	160	0.1848	1226	X-RAY DIFFRACTION	98
7.7944-46.1714	0.1669	117	0.1479	1276	X-RAY DIFFRACTION	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	6.8444	1.2841	-1.4383	5.1207	3.7155	8.1383	0.3468	1.355	-0.1269	-1.3582	-0.2944	-0.0674	-0.1031	-0.1363	-0.0985	0.9495	0.3026	-0.0435	0.7551	0.0808	0.6302	43.0449	80.8031	-22.67
2	5.3743	4.0893	-3.0354	4.232	1.2391	2.7933	0.5538	-0.2095	0.566	-0.7363	-0.8357	-0.7241	-0.1826	0.1193	0.0768	0.7995	0.0364	-0.0111	0.7625	0.1944	0.8225	43.4671	89.1657	-9.7875
3	1.9459	3.9734	1.3289	8.1025	-6.1465	2.0833	0.6456	0.3285	-0.1029	0.1551	-0.5182	0.8224	-0.8937	-0.2843	0.0699	0.6007	0.1015	-0.1541	0.7622	0.0233	0.7424	28.5701	77.5253	-0.2469
4	4.237	0.1167	-1.5487	9.2419	-5.5383	8.2719	-0.2264	-0.8488	-0.5462	0.7372	0.587	2.032	-0.5796	-1.9577	-0.4504	0.8427	0.2931	-0.0399	1.2401	-0.0144	1.3159	7.316	80.0188	-1.461
5	2.7875	-0.1483	5.5126	2.2598	-2.7984	2.4928	-0.686	-0.8611	-1.0637	1.2069	0.468	0.4443	-1.3975	-1.2592	0.335	1.0964	0.336	-0.0116	1.2083	-0.0755	1.029	11.3065	82.8745	5.3348
6	6.1046	-3.503	-1.8888	2.6953	3.6442	9.3163	0.1004	-0.4416	-0.1296	0.8611	-0.5461	-0.1664	-1.205	0.3636	0.511	0.9014	-0.1078	-0.1598	0.6319	0.1716	0.7635	32.0744	73.4589	7.5528
7	5.8451	-1.2221	0.0576	9.6754	0.8628	8.8587	0.0229	-1.061	-0.9865	1.1191	-0.2524	-0.8488	0.1958	0.7812	0.132	0.8761	-0.2013	-0.2335	0.779	0.3539	0.8233	37.2888	66.2432	10.0883
8	2.5949	-2.8724	-4.2745	7.0764	1.7438	9.5127	-0.2065	-0.2588	-0.7246	-0.0859	-0.2731	0.7087	0.3098	0.0825	0.5626	0.5604	-0.0869	-0.2013	0.5893	0.199	1.095	31.7881	59.2298	0.2354
9	2.2881	-3.1082	-5.6526	10.1825	2.8572	5.8304	-0.2138	0.4533	-1.1589	-0.9292	-1.2247	1.2495	-0.7286	-0.6826	1.5374	0.6774	0.1339	-0.3247	0.9143	-0.1052	1.1521	28.5915	61.0405	-8.362
10	2.4029	-1.8493	0.5623	2.4386	-8.1356	8.4613	0.2038	-0.1278	0.296	-0.3585	-0.2329	-0.5918	0.3666	-0.8687	-0.4102	0.7905	0.2021	-0.2344	0.8171	0.0296	0.8505	30.0672	80.3485	-14.3233
11	7.1817	3.641	-0.7812	2.7855	0.0075	5.1073	0.4036	1.575	-0.1469	-0.86	-0.4394	0.6696	0.1604	0.3488	0.14	0.8693	0.3223	-0.2907	0.9865	-0.0613	0.8726	19.6729	86.2247	-14.3232
12	2.5509	-2.1538	1.4117	3.6278	-1.6639	3.2674	1.5011	-0.1107	0.8723	-1.907	-1.1604	0.6952	-1.585	-2.9202	-0.0417	1.7787	1.3255	-0.5112	1.1479	-0.2213	1.1982	12.2659	100.8012	-18.0561
13	8.7925	0.3192	-3.4097	5.7634	-3.6151	8.1018	0.6278	-0.4138	0.6714	1.8036	-0.0369	0.463	-2.4108	-0.0839	-0.5451	2.02	0.3986	-0.1605	0.841	-0.087	0.8676	15.2276	101.0719	-7.1072
14	8.6857	5.8327	0.0903	2.7042	6.9346	7.0057	-0.4742	2.0169	0.0087	0.2311	0.7944	-0.406	-0.5938	-0.0678	-0.2774	0.949	0.3378	-0.205	1.2987	-0.1105	0.7588	15.7334	91.4577	-19.6723

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 94 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 95 through 123 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 124 through 137 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 138 through 203 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 204 through 222 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 6 through 27 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 28 through 81 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 82 through 106 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 107 through 123 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 124 through 137 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 138 through 157 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 158 through 178 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 179 through 203 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 204 through 222 )