PDB-6c1k: HypoPP mutant with ligand1

ID or keywords:

Entry

Database: PDB / ID: 6c1k

Title

HypoPP mutant with ligand1

Components

Ion transport protein

Ion transporter

Keywords

METAL TRANSPORT /

Mutant

Function / homology

Function and homology information

monoatomic cation channel activity / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Arcobacter butzleri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Catterall, W.A. / Zheng, N. / Jiang, D. / Gamal El-Din, T.M.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2018
Title: Structural basis for gating pore current in periodic paralysis.
Authors: Jiang, D. / Gamal El-Din, T.M. / Ing, C. / Lu, P. / Pomes, R. / Zheng, N. / Catterall, W.A.

History

Deposition	Jan 4, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 30, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 6, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6c1k.cif.gz	216.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6c1k.ent.gz	173 KB	Display	PDB format
PDBx/mmJSON format	6c1k.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/c1/6c1k ftp://data.pdbj.org/pub/pdb/validation_reports/c1/6c1k	HTTPS FTP

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Related structure data

Related structure data	6c1eC 6c1mC 6c1pC C: citing same article (ref.)
Similar structure data	4mtf-d 6c1p-d 4ms2-d 4mvu-d 4mtg-d 5kmd-d 4mw3-d 3rvz-1 6c1e-1 4mvr-d 4mto-d 4mvq-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	#243 - Mar 2020 Voltage-gated Sodium Channels similarity (4) #237 - Sep 2019 Nanodiscs and HDL similarity (1)

Deposited unit

A: Ion transport protein

B: Ion transport protein

hetero molecules

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

1

A: Ion transport protein

B: Ion transport protein

hetero molecules

A: Ion transport protein

B: Ion transport protein

hetero molecules

defined by author&software
Evidence: gel filtration
156 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.394, 126.235, 191.525
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

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Protein , 1 types, 2 molecules AB

#1: Protein	Ion transport protein / Ion transporter Mass: 33004.949 Da / Num. of mol.: 2 / Mutation: C235I, H123R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria) Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5

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Non-polymers , 5 types, 30 molecules

#2: Chemical	ChemComp-GAI / GUANIDINE / Guanidine Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₅N₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine Mass: 678.940 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃₆H₇₃NO₈P / Comment: DMPC, phospholipid*YM
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.79 Å³/Da / Density % sol: 78.74 %
Crystal grow	Temperature: 277 K / Method: evaporation / Details: ammonium sulphate, Na-citrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99994 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 26, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99994 Å / Relative weight: 1
Reflection	Resolution: 2.7→42.31 Å / Num. obs: 41173 / % possible obs: 99.6 % / Redundancy: 7.1 % / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.7→2.8 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→42.31 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7

	R_factor	Num. reflection	% reflection
R_free	0.2459	1981	4.81 %
R_work	0.2098	-	-
obs	0.2116	41173	97.01 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→42.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3605	0	449	5	4059

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4130
X-RAY DIFFRACTION	f_angle_d	1.215	5523
X-RAY DIFFRACTION	f_dihedral_angle_d	21.02	1562
X-RAY DIFFRACTION	f_chiral_restr	0.05	615
X-RAY DIFFRACTION	f_plane_restr	0.005	618

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 (%)
2.6988-2.7663	0.3194	144	0.289	2474	X-RAY DIFFRACTION	88
2.7663-2.841	0.298	139	0.2574	2654	X-RAY DIFFRACTION	93
2.841-2.9246	0.2533	135	0.2544	2756	X-RAY DIFFRACTION	98
2.9246-3.019	0.2829	115	0.2416	2892	X-RAY DIFFRACTION	99
3.019-3.1269	0.2399	140	0.2432	2832	X-RAY DIFFRACTION	99
3.1269-3.252	0.2869	156	0.2369	2804	X-RAY DIFFRACTION	99
3.252-3.4	0.2579	159	0.2132	2804	X-RAY DIFFRACTION	99
3.4-3.5791	0.219	170	0.2019	2817	X-RAY DIFFRACTION	99
3.5791-3.8032	0.3286	127	0.2188	2839	X-RAY DIFFRACTION	98
3.8032-4.0967	0.2292	141	0.1829	2857	X-RAY DIFFRACTION	98
4.0967-4.5085	0.2305	123	0.1838	2849	X-RAY DIFFRACTION	98
4.5085-5.1599	0.2287	96	0.1713	2880	X-RAY DIFFRACTION	98
5.1599-6.4972	0.2615	140	0.249	2872	X-RAY DIFFRACTION	97
6.4972-42.3199	0.2231	196	0.205	2862	X-RAY DIFFRACTION	95

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	8.2901	5.3484	-1.9096	5.4766	-4.81	9.8874	0.677	0.5266	-1.6466	0.0901	0.6735	0.0241	0.1827	-0.0926	-0.879	1.8998	0.0684	-0.8117	1.3194	0.3528	1.6561	28.269	24.212	43.1127
2	1.9474	0.3328	0.4512	3.2852	-0.8734	2.7196	0.3203	0.1391	-0.6263	-0.2741	-0.4366	-1.3577	1.4333	1.5872	-0.2713	0.5843	0.1609	-0.163	1.0709	0.1823	1.0236	28.8015	39.6326	21.5317
3	1.1244	-0.5943	0.8427	1.9727	0.4091	2.1079	0.2833	-0.4961	0.1768	0.0458	0.0925	-0.1343	1.1216	-0.7788	-0.0178	1.4025	0.3524	-0.493	0.6625	0.2666	1.2185	20.2859	29.0618	29.3033
4	0.0749	-0.4865	0.4799	3.3761	-3.3032	3.2261	-0.5053	0.7879	-0.3509	-0.4683	-0.8454	0.3388	1.2984	0.5283	0.8376	1.9591	0.4411	-0.0264	1.9962	0.014	1.3237	14.3231	28.2465	11.54
5	4.4427	0.9297	1.4811	3.9065	0.9768	6.1117	-0.2689	0.2422	-0.5268	-0.7476	-0.0027	0.1266	1.3232	1.1667	0.0923	1.1306	0.2155	-0.3865	0.756	0.2823	1.0645	16.8726	37.5056	23.4832
6	1.9413	-0.9588	-1.2915	0.9581	0.2055	2.0364	-0.6372	-0.9301	-0.2376	0.5592	0.5511	-0.0189	-0.4274	0.1418	0.1014	0.7991	-0.0927	-0.0728	0.7058	0.2277	0.6049	-4.525	46.8848	28.7509
7	3.6187	-1.1913	-0.1905	9.9296	-2.3605	8.3034	0.1722	0.1499	-0.6824	-1.4804	0.1977	0.0456	-0.0045	0.0627	-0.2898	0.6836	-0.2075	-0.0405	0.4807	-0.0481	0.6052	-13.8024	49.6162	5.2371
8	1.9755	0.4904	0.5618	2.2028	-0.2879	2.3571	-0.1558	0.1586	-0.1952	-0.0495	0.1402	0.2436	-0.0761	0.0071	-0.0651	0.3268	-0.0004	0.0439	0.3454	0.0583	0.36	-10.9836	56.5478	11.8373
9	3.7275	-0.0267	-0.471	3.4037	-0.1442	1.9464	0.0371	-1.0723	-0.3067	0.922	0.2143	-0.1803	0.057	-0.3842	0.0938	0.7637	0.0035	0.0902	0.7652	0.0994	0.4596	-10.0376	58.1405	28.5888
10	3.6441	-3.9863	3.3834	5.7055	-1.5037	6.7803	0.538	0.438	-0.295	-0.0888	0.2443	-1.2266	0.6345	-0.1652	-0.5183	1.4087	-0.1794	-0.3058	1.7838	-0.6243	1.4519	39.1953	91.4066	43.0023
11	3.1885	-0.156	0.8407	1.8209	0.3029	1.9012	-0.4256	0.3834	1.2136	-0.2075	0.3661	-0.4288	-1.9037	1.3407	-0.1022	1.0925	-0.2288	-0.1461	0.7266	-0.15	0.9729	23.5059	91.8808	21.4981
12	1.0899	0.3482	0.3473	1.9822	-1.1291	5.0612	-0.2766	-0.068	0.7831	0.3023	-0.1813	-0.2782	0.539	0.9551	-0.0307	0.4311	-0.6148	-0.3733	1.5301	-0.7196	1.304	35.2395	86.1768	29.0204
13	2.9392	-0.6622	1.8322	4.0436	-0.5263	2.5458	-0.3061	0.1613	0.0616	0.3195	0.0573	-0.6987	0.0837	1.5079	0.0995	0.8322	-0.1168	-0.2627	1.2022	-0.3396	1.057	29.7439	78.3957	23.8262
14	1.2083	0.5472	-0.4345	1.5584	-0.9602	2.16	0.3708	-0.5351	0.0515	0.4383	-0.3829	0.0255	-0.2559	0.0641	-0.0172	0.6004	0.0475	-0.1708	0.8042	-0.0383	0.5659	16.2959	58.6202	28.7518
15	2.1718	0.865	2.5452	5.3848	-0.403	9.3909	0.2424	1.3516	-0.1355	-0.42	-0.1074	-1.0124	0.1469	-0.1034	-0.317	0.5359	0.2117	0.0149	0.7167	-0.0605	0.6519	13.5338	49.3766	5.2059
16	2.0152	-0.3909	0.3254	1.743	0.3579	2.218	0.0911	-0.2406	-0.3644	-0.0205	-0.0727	-0.2244	0.0857	-0.0766	-0.0976	0.3874	-0.0192	-0.0639	0.2951	0.0405	0.3767	6.5671	52.1463	11.8298
17	2.9801	0.2251	-0.2166	3.3999	-0.4514	1.2674	0.0395	-0.6771	0.3141	1.2008	-0.0026	-0.0945	0.023	0.0041	0.0825	0.7588	0.0269	-0.1271	0.6398	0.0915	0.461	5.0061	53.1236	28.5972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1001 through 1011 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1012 through 1041 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1042 through 1088 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1089 through 1096 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1097 through 1112 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 1113 through 1152 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1153 through 1162 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1163 through 1193 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1194 through 1221 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2001 through 2011 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2012 through 2041 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2042 through 2073 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2074 through 2112 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 2113 through 2152 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 2153 through 2162 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 2163 through 2193 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 2194 through 2221 )

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