PDB-6s5c: Square conformation of KtrA WT ring with bound ATP and calcium

Basic information

• Entry: Database: PDB / ID: 6s5c
• Title: Square conformation of KtrA WT ring with bound ATP and calcium
• Components: Ktr system potassium uptake protein A
• Keywords: TRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / calcium / 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 / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-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 subsp. subtilis str. 168 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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	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 / 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:

• 50.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	50,888	5
Polymers	49,834	2
Non-polymers	1,054	3
Water	0	0

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
• 204 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	203,552	20
Polymers	199,334	8
Non-polymers	4,218	12
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_755	-x+2,-y,z	1
crystal symmetry operation	3_645	-y+1,x-1,z	1
crystal symmetry operation	4_665	y+1,-x+1,z	1

Unit cell

Length a, b, c (Å)	122.693, 122.693, 84.012
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 / Regulatory protein of Ktr cation channel

Details:

Mass: 24916.760 Da / Num. of mol.: 2
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

A-601 B-601 ChemComp-ATP / ADENOSINE-5'-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-602 ChemComp-CA / CALCIUM ION

Details:

Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

• Has ligand of interest: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.17 ų/Da / Density % sol: 61.23 %
• Crystal grow: Temperature: 293.15 K / Method: vapor diffusion, sitting drop; Details: 100mM HEPES-NaOH pH 8.0, 5% PEG 6000, 2.5% 2-Methyl-2,4-pentanediol (MPD)

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2016
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97857 Å / Relative weight: 1
• Reflection: Resolution: 3→45.94 Å / Num. obs: 12614 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.043 / R_pim(I) all: 0.021 / R_rim(I) all: 0.046 / Net I/σ(I): 24.5
• Reflection shell: Resolution: 3→3.18 Å / Redundancy: 9.8 % / R_merge(I) obs: 1.418 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1996 / CC_1/2: 0.658 / R_pim(I) all: 0.475 / % possible all: 98.9

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: 6S2J

6s2j

Resolution: 3→37.808 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 0.5 / Phase error: 33.9

	Rfactor	Num. reflection	% reflection
Rfree	0.2588	1906	7.76 %
Rwork	0.207	-	-
obs	0.2108	12614	99.67 %

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

Refinement step

Cycle: LAST / Resolution: 3→37.808 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3412	0	63	0	3475

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3534
X-RAY DIFFRACTION	f_angle_d	0.697	4788
X-RAY DIFFRACTION	f_dihedral_angle_d	13.136	1320
X-RAY DIFFRACTION	f_chiral_restr	0.026	552
X-RAY DIFFRACTION	f_plane_restr	0.002	600

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.9963-3.0712	0.4355	142	0.3418	1549	X-RAY DIFFRACTION	97
3.0712-3.1542	0.4113	154	0.3383	1659	X-RAY DIFFRACTION	100
3.1542-3.2469	0.4096	84	0.3395	1676	X-RAY DIFFRACTION	100
3.2469-3.3517	0.3886	120	0.3383	1611	X-RAY DIFFRACTION	100
3.3517-3.4714	0.3512	136	0.2857	1610	X-RAY DIFFRACTION	100
3.4714-3.6103	0.4307	163	0.2878	1624	X-RAY DIFFRACTION	100
3.6103-3.7744	0.3195	151	0.2687	1563	X-RAY DIFFRACTION	100
3.7744-3.9732	0.3374	164	0.2752	1616	X-RAY DIFFRACTION	100
3.9732-4.2219	0.2329	122	0.2387	1646	X-RAY DIFFRACTION	100
4.2219-4.5473	0.2718	108	0.1904	1632	X-RAY DIFFRACTION	100
4.5473-5.004	0.2522	121	0.1849	1621	X-RAY DIFFRACTION	100
5.004-5.726	0.2586	166	0.1975	1602	X-RAY DIFFRACTION	100
5.726-7.2059	0.2212	144	0.222	1611	X-RAY DIFFRACTION	100
7.2059-37.8105	0.1963	131	0.1516	1624	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	6.1944	-2.8246	1.4218	6.1421	1.431	9.8877	-1.0646	1.2435	-0.0821	-1.7648	0.7403	0.2318	-0.8778	0.6133	0.2573	1.295	-0.5825	-0.0401	1.4994	0.1937	0.9364	140.6134	19.8548	-25.3178
2	2.2524	-2.1793	-0.1108	2.2729	-1.2102	2.1815	-1.3999	1.3858	-1.811	-1.0734	1.175	-1.6047	-0.0326	1.6038	0.148	1.0368	-0.2308	0.2084	1.5425	-0.132	1.0544	148.5199	10.2471	-16.5373
3	6.4796	1.2003	-2.163	5.9184	4.7334	5.4684	-0.723	0.6395	-0.5711	0.1909	0.5926	-0.4797	0.3406	0.9529	0.3066	0.9946	0.0106	0.1389	1.0905	0.3376	1.0591	146.6217	22.5282	-8.3258
4	6.3387	0.8078	-5.6943	5.0474	3.0786	8.1319	0.2408	-0.8095	0.8815	1.3106	-0.4848	0.1737	-1.5595	1.2743	0.314	1.4728	-0.3798	-0.2893	1.1361	0.2233	1.3892	141.5239	53.1332	-1.2585
5	7.1234	3.8813	4.8415	6.7807	1.2456	5.7603	-0.3512	-0.8342	-0.2518	1.2646	-0.1427	0.563	1.0408	1.1966	0.4864	1.1677	0.2266	0.4265	1.3031	0.3294	1.0303	133.5018	25.0778	8.0642
6	9.3347	-0.2021	1.5902	4.9307	1.3355	8.5908	-0.5085	-0.5098	0.3296	1.0706	-0.4981	2.066	0.8352	-0.9423	0.9238	1.0067	-0.0129	0.5008	1.1048	0.0444	1.6426	120.6333	27.8892	2.8658
7	9.3777	5.3174	-5.5422	4.2705	2.8345	2.435	-0.8029	0.1849	0.4641	-0.4805	0.0531	0.7291	-0.1517	0.3598	0.7628	1.051	-0.2444	-0.1577	1.0881	0.578	1.2958	130.0306	32.3571	-12.3826
8	8.9389	2.257	-1.7244	10.6514	5.8396	7.1413	-1.5305	2.7939	1.3269	-2.5254	1.7704	-0.9237	-1.8739	1.2473	-0.2063	1.7549	-0.9391	-0.1416	1.9468	0.3896	1.5124	154.3832	45.5012	-17.5461
9	2.8452	-4.8507	-1.0644	4.5494	5.1282	3.327	-0.3099	-0.5067	0.3513	-1.767	1.2414	-0.3729	-0.6592	0.2544	-0.8706	1.5477	-0.8243	-0.0859	2.0172	0.36	1.3654	157.7056	45.9791	-14.0557

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 94 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 95 through 137 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 138 through 222 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 54 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 55 through 106 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 107 through 137 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 138 through 178 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 179 through 222 )