PDB-2wli: POTASSIUM CHANNEL FROM MAGNETOSPIRILLUM MAGNETOTACTICUM

ID or keywords:

Entry

Database: PDB / ID: 2wli

Title

POTASSIUM CHANNEL FROM MAGNETOSPIRILLUM MAGNETOTACTICUM

Components

KIRBAC3.1 POTASSIUM CHANNEL
POTASSIUM CHANNEL

Keywords

METAL TRANSPORT / INTEGRAL MEMBRANE PROTEIN / IONIC CHANNEL / ION TRANSPORT / 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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.09 Å

Authors

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

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2010
Title: Domain Reorientation and Rotation of an Intracellular Assembly Regulate Conduction in Kir Potassium Channels.
Authors: Clarke, O.B. / Caputo, A.T. / Hill, A.P. / Vandenberg, J.I. / Smith, B.J. / Gulbis, J.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	Jun 27, 2012	Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	May 29, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 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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PDBx/mmCIF format	2wli.cif.gz	225.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2wli.ent.gz	182.6 KB	Display	PDB format
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Validation report

Summary document	2wli_validation.pdf.gz	443.2 KB	Display	wwPDB validaton report
Full document	2wli_full_validation.pdf.gz	468.9 KB	Display
Data in XML	2wli_validation.xml.gz	24 KB	Display
Data in CIF	2wli_validation.cif.gz	31.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wl/2wli ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wli	HTTPS FTP

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Related structure data

Related structure data	2wlhC 2wljC 2wlkC 2wllC 2wlmC 2wlnC 2wloC 2x6aC 2x6bC 2x6cC 1xl4S 1xl6 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2wlj-d 1xl6-d 2wlo-d 5hc9-1 1xl4-d 6o9v-d 4qik-d 1ryd-d 1h6a-d 3imq-d 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) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (2)

Deposited unit

A: POTASSIUM CHANNEL

B: KIRBAC3.1 POTASSIUM CHANNEL

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	113.409, 105.009, 89.422
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-1302- K
4	1	A-1303- K

#1: Protein	POTASSIUM CHANNEL / KIRBAC3.1 Mass: 33826.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria) Description: EXPRESSED RECOMBINANTLY IN ESCHERICHIA COLI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: D9N164*PLUS
#2: Protein	KIRBAC3.1 POTASSIUM CHANNEL Mass: 33782.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-TERMINAL HEXAHISTIDINE TAG APPENDED Source: (gene. exp.) MAGNETOSPIRILLUM MAGNETOTACTICUM (bacteria) Description: EXPRESSED RECOMBINANTLY IN ESCHERICHIA COLI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: D9N164*PLUS
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	RESIDUES 5-295 CORRESPOND TO GENBANK ACCESSION ZP_00055625, CHAIN A INCLUDES LEU200ARG CONFLICT.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.44 Å³/Da / Density % sol: 72 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 7.5 Details: PRECIPITANT: 15 % PEG 400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN: 8MG/ML KIRBAC3.1 150MM KCL 20MM TRIS8.0 0.05% TDM 4MM LDAO PROTEIN AND PRECIPITANT WERE ...Details: PRECIPITANT: 15 % PEG 400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN: 8MG/ML KIRBAC3.1 150MM KCL 20MM TRIS8.0 0.05% TDM 4MM LDAO PROTEIN AND PRECIPITANT WERE COMBINED IN A 1:1 RATIO AND EQUILIBRATED AGAINST A RESERVOIR OF PRECIPITANT IN A SITTING-DROP VAPOUR-DIFFUSION SET-UP.

Crystal

Density Matthews: 4.44 Å³/Da / Density % sol: 72 % / Description: NONE

Crystal grow

Method: vapor diffusion, sitting drop / pH: 7.5
Details: PRECIPITANT: 15 % PEG 400 2.5 % PEG 4000 2.5 % PEG 8000 10 % GLYCEROL 90 MM HEPES PH 7.5 PROTEIN: 8MG/ML KIRBAC3.1 150MM KCL 20MM TRIS8.0 0.05% TDM 4MM LDAO PROTEIN AND PRECIPITANT WERE ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953639
Detector	Type: ADSC CCD / Detector: CCD / Date: May 18, 2008 / Details: MIRRORS
Radiation	Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.953639 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 20089 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.13 / Net I/σ(I): 16.6
Reflection shell	Resolution: 3.1→3.21 Å / Redundancy: 8.1 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XL4

1xl4

Resolution: 3.09→15 Å / Cor.coef. F_o:F_c: 0.876 / Cor.coef. F_o:F_c free: 0.841 / SU B: 47.031 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R: 1.322 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28767	998	5 %	SHELLS
R_work	0.26538	-	-	-
obs	0.26655	18847	100 %	-

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: 32.917 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.87 Å²	0 Å²	0 Å²
2-	-	1.02 Å²	0 Å²
3-	-	-	-3.89 Å²

Refinement step

Cycle: LAST / Resolution: 3.09→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4261	0	4	2	4267

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.021	4395
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	4010
X-RAY DIFFRACTION	r_angle_refined_deg	1.339	1.932	5989
X-RAY DIFFRACTION	r_angle_other_deg	3.098	3	9213
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.614	5	547
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.641	22.165	194
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.349	15	667
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.096	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	693
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4905
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	979
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	0	1.5	2719
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	1114
X-RAY DIFFRACTION	r_mcangle_it	0	2	4382
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0	3	1676
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0	4.5	1604
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: 3.094→3.17 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0	0	-
R_work	0.335	1309	-
obs	-	-	100 %

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	0.2848	-0.4503	1.0035	1.6449	-1.1617	4.3191	0.0572	-0.0126	-0.0881	0.2461	-0.1269	0.2494	0.4939	-0.0071	0.0697	0.1655	-0.0257	0.0923	0.1189	0.0083	0.2444	-22.539	-60.6104	17.4741
2	0.4023	-0.147	-0.4124	0.4199	0.6006	1.0319	0.0743	0.041	-0.0126	0.181	-0.1054	0.0977	0.2265	-0.077	0.0311	0.2084	-0.045	-0.0653	0.2717	-0.0423	0.2165	-14.0652	-62.9818	45.4444
3	3.9432	-0.6443	-6.224	8.5624	4.0825	10.9359	-0.1671	-0.1395	-0.1929	0.9624	0.0045	-0.3396	0.6065	0.2051	0.1626	0.1777	-0.117	-0.0576	0.2694	0.042	0.1107	-9.126	-66.835	66.6736
4	1.8045	1.6833	-1.1833	1.8528	-1.3314	0.9608	-0.3083	0.3574	0.1491	-0.1626	0.4184	0.1641	0.1131	-0.3071	-0.1101	0.2068	-0.061	0.0204	0.1833	0.0218	0.0731	-9.2159	-60.1586	57.1848
5	1.3841	0.3271	0.1412	0.254	1.1192	6.8191	0.0009	0.0341	-0.119	0.026	0.0333	-0.0163	0.1397	0.1532	-0.0342	0.0837	-0.0131	0.0084	0.0194	0.0067	0.0785	-0.7542	-66.058	57.6317
6	3.0527	1.5133	-0.6169	3.9615	-5.009	7.7332	0.5022	0.2357	0.036	-0.2058	-0.232	0.3034	0.4802	0.2457	-0.2702	0.1569	0.1133	-0.0526	0.123	-0.0753	0.0593	-7.0102	-55.1383	34.0923
7	2.5508	-0.5766	1.0256	2.3081	0.4956	4.5753	-0.0276	0.1963	0.0468	-0.1476	-0.0216	0.0259	-0.2345	0.0269	0.0492	0.0187	-0.0011	-0.0038	0.0163	0.0038	0.0018	-19.5964	-41.6258	2.1489
8	0.4815	-0.6126	-0.9468	5.9398	2.6432	3.4475	-0.016	-0.0416	-0.028	0.246	-0.0614	0.093	0.1881	0.0134	0.0774	0.0264	-0.0276	0.0032	0.0637	-0.0087	0.0323	-25.5251	-65.0108	-7.6387
9	1.6747	-0.9328	2.113	9.4976	-2.0163	2.7459	0.1379	0.0135	-0.2468	0.2664	0.1737	0.0171	0.1305	0.0034	-0.3116	0.132	0.0124	0.0506	0.0453	-0.0316	0.1739	-17.9627	-19.0636	9.6404
10	3.7329	-1.7527	0.2157	7.6683	-4.3829	2.7586	-0.266	0.2498	0.138	-0.4174	0.3225	0.0593	0.19	-0.3655	-0.0566	0.3466	0.1042	-0.0161	0.2765	-0.0888	0.1871	-13.3885	-33.5902	23.5001
11	0.4347	0.0367	0.2943	1.9472	-0.5052	1.5659	-0.1472	-0.0814	0.2291	-0.176	0.2887	0.0869	0.2771	-0.2907	-0.1415	0.2859	0.0036	-0.0854	0.1146	0.0152	0.2298	-10.5499	-38.3603	45.4714
12	4.7438	0.9042	2.0398	1.1764	2.4984	5.3094	0.1581	-0.1047	-0.0976	-0.0007	0.0048	-0.0749	0.0016	0.0078	-0.1629	0.0444	0.0135	0.0226	0.0497	0.0046	0.0385	-14.3151	-43.4297	66.6976
13	3.0011	-4.4576	-0.4285	6.6392	0.5686	0.5608	0.054	0.1138	-0.1125	-0.0077	-0.1691	0.1825	-0.3811	-0.1556	0.1151	0.3259	0.0617	-0.0104	0.143	-0.0523	0.1477	-7.6639	-43.2681	57.1893
14	1.783	1.4306	-0.4063	2.3353	-0.5234	6.5133	0.0318	-0.1557	0.138	0.2469	-0.1644	0.2946	0.2646	-0.3552	0.1326	0.0721	0.0131	0.0553	0.1993	-0.0335	0.0697	-13.5472	-51.7486	57.6109
15	3.3636	-1.004	-3.5715	4.5476	-0.2258	7.2579	-0.7075	-0.2187	0.3085	-0.2159	0.4675	-0.488	0.3409	-0.1167	0.24	0.2878	0.0511	-0.0988	0.0868	-0.0767	0.1416	-2.9183	-45.5977	34.351
16	1.8791	0.2884	-0.5307	2.5332	-1.4908	5.3186	-0.0495	0.0071	0.1032	-0.0193	0.0645	0.2731	-0.2967	-0.0843	-0.015	0.0258	0.0022	-0.0123	0.0025	0.0036	0.0454	11.0791	-33.7817	2.1259
17	9.5551	-1.3917	-6.4336	10.0205	-8.7001	13.792	-0.9018	0.4935	0.3068	-0.0183	-0.3565	-1.5247	0.7504	-0.0545	1.2583	0.4286	-0.0618	-0.048	0.4516	0.0823	0.5569	-6.7296	-25.0071	-2.7324
18	10.296	-2.9277	-1.8076	0.9046	0.6533	0.5872	0.0852	-0.2312	0.1572	0.0209	0.1168	-0.1383	0.0755	0.1421	-0.202	0.0634	0.0108	-0.0468	0.1118	-0.0202	0.1765	33.3846	-38.9896	8.8091

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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