PDB-2wlj: Potassium channel from Magnetospirillum magnetotacticum

ID or keywords:

Entry

Database: PDB / ID: 2wlj

Title

Potassium channel from Magnetospirillum magnetotacticum

Components

POTASSIUM CHANNEL

Keywords

METAL TRANSPORT

Function / homology

Function and homology information

inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding
Similarity search - Function

Biological species

MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Clarke, O.B. / Caputo, A.T. / Smith, B.J. / Gulbis, J.M.

Citation

Journal: To be Published
Title: Two Intermediate Gating State Crystal Structures of the Kirbac3.1 K+ Channel
Authors: Gulbis, J.M. / Kuo, A. / Smith, B. / Doyle, D.A. / Edwards, A. / Arrowsmith, C. / Sundstrom, M.

History

Deposition	Jun 24, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Apr 25, 2012	Group: Atomic model / Database references ...Atomic model / Database references / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2	Jan 30, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3	Feb 6, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 0

THIS ENTRY 2WLJ REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R1XL4SF) ...

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wlj.cif.gz	243.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2wlj.ent.gz	200 KB	Display	PDB format
PDBx/mmJSON format	2wlj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/2wlj ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlj	HTTPS FTP

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Related structure data

Related structure data	2wlhC 2wliC 2wlkC 2wllC 2wlmC 2wlnC 2wloC 2x6aC 2x6bC 2x6cC 1p7bS 1xl4 1xl6 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2wlh-1 6o9u-1 1xl4-1 1t7l-d 4zo8-d 2x6a-1 6kj0-d 2wlm-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 (2) #15 - Mar 2001 Transfer RNA similarity (1) #23 - Nov 2001 DNA similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (2)

Deposited unit

A: POTASSIUM CHANNEL

B: POTASSIUM CHANNEL

hetero molecules

68 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: POTASSIUM CHANNEL

B: POTASSIUM CHANNEL

hetero molecules

A: POTASSIUM CHANNEL

B: POTASSIUM CHANNEL

hetero molecules

defined by author&software
136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	105.627, 109.385, 88.786
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-1300- K
2	1	A-1301- K
3	1	A-1305- CA

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Protein , 1 types, 2 molecules AB

#1: Protein	POTASSIUM CHANNEL / / KIRBAC3.1 Mass: 33782.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: D9N164*PLUS

#1: Protein

POTASSIUM CHANNEL /

/ KIRBAC3.1

Mass: 33782.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED
Source: (gene. exp.)

MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria)
Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: D9N164*PLUS

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Non-polymers , 5 types, 180 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-SPM / SPERMINE / Spermine Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₆N₄
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	RESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.8 Å³/Da / Density % sol: 65 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1XL4.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 90MM HEPES, 2.5% PEG 8000, 2.5% PEG 4000, 20% PEG 400, 12.5MM MAGNESIUM CHLORIDE, 42.5MM MAGNESIUM ACETATE, 2.5% GLYCEROL, 14MM HEGA-10, PH 7.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 2.6→26 Å / Num. obs: 29551

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
MOSFLM		data reduction
SCALA		data scaling
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7B

1p7b

Resolution: 2.6→15 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.928 / SU B: 17.526 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.42 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. THIS ENTRY IS A RE-REFINEMENT OF PDB ENTRY 1XL4. IMPROVED REFINEMENT STATISTICS WERE OBTAINED ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24331	1525	5.2 %	RANDOM
R_work	0.22028	-	-	-
obs	0.22148	27897	91.58 %	-

Solvent computation

Ion probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 78.133 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.57 Å²	0 Å²	0 Å²
2-	-	0.87 Å²	0 Å²
3-	-	-	-1.44 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4331	0	20	173	4524

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	4562
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.477	1.934	6207
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.821	5	569
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.239	21.932	207
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.305	15	716
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.804	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	708
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	3452
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.334	1.5	2769
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.083	2	4482
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.128	3	1793
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.209	4.5	1714
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.6→2.666 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.391	122	-
R_work	0.328	1771	-
obs	-	-	82.52 %

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	0.1462	0.4983	0.3902	1.7075	1.3411	1.0552	0.0056	-0.0195	0.0504	0.0577	-0.0826	0.134	0.0487	-0.0616	0.077	0.019	-0.0305	-0.0383	0.0503	0.0552	0.201	45.7151	-77.8281	204.3821
2	3.4648	-0.9597	5.1033	0.9008	-1.1219	8.0739	0.005	0.2517	-0.0615	0.219	-0.0631	0.1989	0.35	0.2835	0.058	0.2286	-0.0469	0.0845	0.0379	-0.0183	0.0799	47.0158	-71.0043	176.0112
3	6.1866	2.9694	-1.8686	1.9504	-2.1894	3.7547	-0.0336	0.6602	0.1174	-0.0766	0.3629	0.185	0.1255	-0.2971	-0.3293	0.0771	0.0091	-0.0527	0.0775	0.0121	0.0543	42.252	-67.3206	154.567
4	2.4106	2.5813	1.3382	3.0582	1.343	0.772	0.1159	0.1003	-0.1163	-0.0629	-0.0181	0.0214	0.0988	0.1058	-0.0978	0.1914	0.0284	-0.0819	0.108	-0.0796	0.079	48.4201	-65.708	164.1201
5	3.3534	0.4528	0.4209	3.5366	0.178	0.0573	0.2088	0.2405	-0.2486	0.1377	-0.2042	0.6752	0.0333	0.0212	-0.0046	0.0624	-0.0092	-0.0087	0.0771	-0.0538	0.1698	40.3444	-59.5661	164.4426
6	7.0928	-2.6606	7.6082	2.272	-3.008	8.1862	0.2073	-0.0802	-0.0351	-0.0218	-0.1574	0.0789	0.1948	-0.0746	-0.0499	0.0793	0.0248	0.0145	0.0476	-0.0024	0.006	51.9403	-61.7454	188.2817
7	0.1212	-0.188	0.0026	0.5129	-0.2887	0.8256	0.0299	-0.033	0.0348	-0.0355	0.03	0.0623	0.0898	0.1279	-0.0599	0.0344	0.0148	0.0263	0.033	-0.0046	0.0892	62.2344	-75.134	220.2313
8	7.3102	-3.8849	-2.9016	2.1521	1.7868	2.3498	0.0777	0.1788	-0.0733	-0.0375	-0.0036	0.0186	-0.0117	-0.0069	-0.0741	0.0014	-0.003	0.0006	0.1462	0.0083	0.0534	37.7897	-78.9431	229.7489
9	6.1668	-4.2251	-2.695	2.923	2.1552	4.5459	0.02	0.0716	-0.0379	-0.0443	-0.0612	0.0286	-0.3133	-0.1177	0.0412	0.0286	0.0138	0.0031	0.028	0.0242	0.0264	85.1541	-75.8257	210.3411
10	0.9078	-0.7181	0.9461	0.5717	-0.7488	0.9862	-0.4581	-0.0267	0.2616	0.4638	0.0959	-0.1688	-0.5749	-0.0249	0.3622	0.5994	-0.0593	0.1483	0.178	-0.1843	0.4815	33.3781	-42.877	197.4337
11	1.0076	1.5814	-1.3578	2.6075	-2.8058	5.5632	-0.1467	-0.2064	0.0679	-0.3094	-0.1243	0.0413	0.4011	-0.7263	0.271	0.058	0.008	0.0142	0.3283	-0.0954	0.0403	36.5666	-48.7602	175.8991
12	1.1559	-2.851	-2.0202	7.0347	4.9826	3.5309	0.1951	0.0451	0.0453	-0.5077	-0.107	-0.1017	-0.3521	-0.079	-0.0881	0.0847	-0.0024	-0.0197	0.0868	0.0554	0.045	40.0023	-44.0161	154.6615
13	7.5212	-0.0146	1.1684	0.002	-0.0039	0.1949	-0.0127	0.2361	0.2282	-0.0087	0.0013	0.0079	0.0336	0.0614	0.0114	0.0997	0.0307	-0.059	0.1418	0.022	0.0503	41.9499	-50.2361	164.0562
14	5.005	0.1007	0.4075	3.3023	-1.4222	0.6632	-0.1735	0.0016	0.8887	-0.037	0.2769	0.4693	0.0074	-0.0919	-0.1034	0.0464	0.0163	-0.0277	0.0738	0.0557	0.2268	47.9669	-42.0529	164.4215
15	4.6352	3.9654	-3.6526	9.1156	-8.4067	7.7534	0.2005	-0.1264	-0.1293	0.1011	-0.1089	0.0976	-0.096	0.1036	-0.0916	0.0338	-0.0396	-0.0066	0.0516	0.0013	0.0113	45.6229	-53.5128	188.2469
16	0.2011	0.0199	-0.0693	0.0793	-0.1626	0.8242	-0.003	-0.0013	0.1083	-0.0075	-0.0166	-0.04	0.1381	-0.0906	0.0196	0.0318	-0.0284	-0.0071	0.0455	0.0174	0.0962	33.1343	-63.8792	220.4593
17	3.4443	5.0393	1.4815	9.1616	4.0532	2.626	-0.0569	-0.1377	0.2508	-0.3163	-0.1284	0.4452	-0.2631	0.0214	0.1852	0.0506	0.0222	-0.0476	0.0527	-0.0616	0.0931	28.3693	-39.7609	229.889
18	2.4893	-1.2295	-0.2587	6.2881	1.8703	2.8998	0.042	-0.0944	-0.1204	0.3329	0.0906	0.0415	0.1624	-0.011	-0.1326	0.0254	-0.0006	-0.0045	0.005	0.005	0.0179	36.2786	-86.9096	213.6158

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	12 - 43
2	X-RAY DIFFRACTION	2	A	44 - 71
3	X-RAY DIFFRACTION	3	A	72 - 81
4	X-RAY DIFFRACTION	4	A	82 - 100
5	X-RAY DIFFRACTION	5	A	101 - 120
6	X-RAY DIFFRACTION	6	A	121 - 137
7	X-RAY DIFFRACTION	7	A	138 - 182
8	X-RAY DIFFRACTION	7	A	194 - 274
9	X-RAY DIFFRACTION	7	A	286 - 299
10	X-RAY DIFFRACTION	8	A	183 - 193
11	X-RAY DIFFRACTION	9	A	275 - 285
12	X-RAY DIFFRACTION	10	B	12 - 43
13	X-RAY DIFFRACTION	11	B	44 - 71
14	X-RAY DIFFRACTION	12	B	72 - 81
15	X-RAY DIFFRACTION	13	B	82 - 100
16	X-RAY DIFFRACTION	14	B	101 - 120
17	X-RAY DIFFRACTION	15	B	121 - 137
18	X-RAY DIFFRACTION	16	B	138 - 182
19	X-RAY DIFFRACTION	16	B	194 - 274
20	X-RAY DIFFRACTION	16	B	286 - 299
21	X-RAY DIFFRACTION	17	B	183 - 193
22	X-RAY DIFFRACTION	18	B	275 - 285

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 180 molecules

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Details

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Experiment

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Data collection

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