PDB-6c1m: NavAb NormoPP mutant

ID or keywords:

Entry

Database: PDB / ID: 6c1m

Title

NavAb NormoPP mutant

Components

Ion transport protein

Keywords

METAL TRANSPORT / Mutant

Function / homology

Function and homology information

voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function

Biological species

Arcobacter butzleri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.518 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	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6c1m.cif.gz	228.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6c1m.ent.gz	182.6 KB	Display	PDB format
PDBx/mmJSON format	6c1m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6c1m_validation.pdf.gz	4.7 MB	Display	wwPDB validaton report
Full document	6c1m_full_validation.pdf.gz	4.7 MB	Display
Data in XML	6c1m_validation.xml.gz	30 KB	Display
Data in CIF	6c1m_validation.cif.gz	36.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c1/6c1m ftp://data.pdbj.org/pub/pdb/validation_reports/c1/6c1m	HTTPS FTP

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Related structure data

Related structure data	6c1eC 6c1kC 6c1pC 3rvyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5kmf-d 4ekw-2 6c1e-1 5kmh-d 5kmd-d 4mvm-d 4ekw-1 4mw3-d 5klg-d 4mw8-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

81.7 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
163 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.330, 126.244, 191.585
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 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 , 6 types, 63 molecules

#2: Chemical	ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE Mass: 678.940 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃₆H₇₃NO₈P / Comment: DMPC, phospholipid*YM
#3: Chemical	ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium Mass: 631.884 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃₂H₅₉N₂O₈S / Comment: detergent*YM
#4: Chemical	ChemComp-MGX / 1-METHYLGUANIDINE Mass: 73.097 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₇N₃
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / 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 / pH: 4.8 / 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: Oct 11, 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: 2.52→42.31 Å / Num. obs: 51039 / % possible obs: 99.4 % / Redundancy: 5.3 % / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.52→2.64 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
Starting model: 3RVY

3rvy

Resolution: 2.518→42.311 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2266	2499	4.9 %
R_work	0.2031	-	-
obs	0.2043	51039	97.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.518→42.311 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3674	0	631	32	4337

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4424
X-RAY DIFFRACTION	f_angle_d	1.253	5955
X-RAY DIFFRACTION	f_dihedral_angle_d	21.512	1620
X-RAY DIFFRACTION	f_chiral_restr	0.054	685
X-RAY DIFFRACTION	f_plane_restr	0.005	635

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 (%)
2.5175-2.5659	0.3221	110	0.3419	1850	X-RAY DIFFRACTION	69
2.5659-2.6183	0.3485	150	0.3088	2622	X-RAY DIFFRACTION	98
2.6183-2.6752	0.3435	153	0.3002	2686	X-RAY DIFFRACTION	99
2.6752-2.7374	0.3264	142	0.2637	2728	X-RAY DIFFRACTION	100
2.7374-2.8059	0.2457	160	0.2349	2677	X-RAY DIFFRACTION	100
2.8059-2.8817	0.2323	126	0.2268	2743	X-RAY DIFFRACTION	100
2.8817-2.9665	0.2323	125	0.2185	2737	X-RAY DIFFRACTION	100
2.9665-3.0622	0.2283	114	0.2215	2747	X-RAY DIFFRACTION	100
3.0622-3.1716	0.2345	151	0.2123	2747	X-RAY DIFFRACTION	100
3.1716-3.2986	0.2533	149	0.2025	2713	X-RAY DIFFRACTION	100
3.2986-3.4486	0.2197	158	0.1818	2735	X-RAY DIFFRACTION	100
3.4486-3.6304	0.1846	153	0.1729	2741	X-RAY DIFFRACTION	100
3.6304-3.8577	0.232	120	0.1806	2763	X-RAY DIFFRACTION	100
3.8577-4.1553	0.1862	131	0.1695	2756	X-RAY DIFFRACTION	100
4.1553-4.573	0.2166	130	0.1843	2773	X-RAY DIFFRACTION	100
4.573-5.2337	0.2155	85	0.177	2868	X-RAY DIFFRACTION	100
5.2337-6.5899	0.2387	146	0.2475	2804	X-RAY DIFFRACTION	100
6.5899-42.3173	0.2177	196	0.203	2850	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	8.5166	7.0626	4.4251	8.6792	1.625	3.6837	1.6425	-0.1994	2.3355	-0.4017	0.4552	0.2268	0.2241	0.8258	-1.4135	2.2074	0.054	0.8533	1.3521	-0.6131	1.7247	35.1501	39.1861	234.8
2	5.6562	-1.7714	-4.18	9.4916	3.0151	3.4293	0.2826	0.3111	0.6981	-0.4453	-0.8911	1.648	-2.0517	-2.8028	0.5251	0.6439	0.2881	0.1608	1.116	-0.138	1.0277	34.3882	23.5314	213.1555
3	8.7735	-1.2365	5.4274	2.4086	0.2015	4.4353	-0.7651	0.8824	1.6263	0.1049	-0.1627	1.0228	-0.6026	1.5308	0.6519	1.6151	0.5063	0.6358	0.9905	-0.3177	1.381	40.0612	35.2293	220.6234
4	2.9593	-2.8737	2.4877	5.9713	-0.6923	3.2545	0.5009	0.4398	0.6728	-0.5146	-0.6132	-0.4865	-0.9661	1.5821	-0.0516	1.3428	0.0997	0.4359	1.5296	-0.3192	1.117	48.8232	32.6735	215.5646
5	9.4135	-1.1091	-2.7013	9.0516	-0.8327	7.6717	0.6172	-0.3897	1.5744	-0.6117	0.0762	1.4645	-2.0328	-1.6727	-0.4776	0.9915	0.1964	0.2738	0.711	-0.338	1.0095	46.2548	25.5986	215.0988
6	9.0492	-1.1821	-2.3795	2.2417	1.384	8.4335	-0.5814	-1.4136	0.4028	0.5684	0.5888	0.135	0.1126	0.4522	-0.1821	0.8418	-0.0273	0.0222	0.4185	-0.1203	0.5055	67.6937	16.2753	220.3459
7	2.5938	-2.8946	-3.2347	3.278	3.4254	4.0895	0.2093	0.8743	0.4578	-0.8595	-0.0359	-0.2387	1.0001	0.1055	-0.2413	0.7734	-0.1275	0.0278	0.6307	0.0155	0.5122	76.8915	13.4005	196.927
8	4.8654	-0.1796	-1.8629	6.2178	0.5188	2.5893	-0.0886	-0.0377	0.2154	0.1187	0.083	-0.2208	0.1221	0.2782	0.0094	0.3722	-0.0159	-0.0791	0.4666	-0.026	0.3059	74.1567	6.5662	203.4242
9	7.0076	-0.7749	0.0495	7.9352	0.5397	5.0978	-0.0761	-2.0056	0.6202	1.5697	0.0955	0.5928	-0.0232	-0.024	0.0957	0.8167	0.0329	-0.0953	0.903	-0.1848	0.4668	73.1947	5.0175	220.1103
10	8.5923	-6.8613	-4.5961	5.4812	3.6661	2.4975	0.3899	-0.3032	0.1151	-0.7849	0.9852	1.9077	-0.4776	-0.4502	-1.5299	1.4714	-0.2986	0.3316	2.1529	0.7315	1.5367	23.8941	-27.9614	234.8536
11	6.2999	-0.3792	-2.6887	5.3173	-1.973	3.347	-0.6965	0.693	-1.2743	-0.6231	0.5558	0.5059	3.1116	-2.8898	0.1831	1.0328	-0.3111	0.0629	0.7151	0.1195	1.0026	39.6238	-28.793	213.0989
12	5.154	2.4659	-0.5037	8.5707	4.3967	4.2057	0.3245	0.0023	0.0879	-0.3309	-0.1949	0.5823	-1.3188	-1.5922	-0.0067	0.9193	-0.3221	0.2733	1.5545	0.6193	1.2499	29.0871	-20.3696	221.2068
13	3.6662	4.4264	-2.4673	9.2604	-6.0814	6.1688	-3.3886	5.4622	0.5213	-3.6311	3.5821	1.6037	4.1173	-4.6733	-0.5104	2.2899	-0.8938	0.0706	3.1241	0.5444	1.502	28.1546	-15.0873	204.8159
14	7.3549	-1.4766	1.424	7.1899	-4.3348	3.0864	-0.0829	0.658	-1.1063	0.55	0.75	1.4687	1.0615	-2.1909	-0.494	0.7993	-0.1406	0.2756	1.02	0.2686	1.0526	37.5461	-16.8533	215.1082
15	2.3138	1.0567	-0.7417	9.9168	-3.8333	9.5527	0.5633	-0.6209	-0.091	1.0264	-0.4735	0.25	-0.1219	0.1008	-0.2827	0.4523	0.0515	0.1216	0.8565	0.0145	0.4958	46.8783	4.5259	220.3368
16	3.5495	2.6399	-3.2307	1.9841	-2.4411	3.5007	0.1277	0.2523	0.2454	-1.1059	0.3732	0.4853	-0.1479	0.299	-0.5659	0.6375	0.1508	-0.0475	0.8099	0.0153	0.5105	49.787	13.7336	196.9244
17	4.3087	0.1582	-0.767	4.2991	1.0374	2.9952	0.2074	-0.8414	0.1131	0.7942	-0.1454	0.4022	0.0885	0.076	-0.048	0.5362	-0.0304	0.0919	0.5481	-0.0566	0.3379	57.2731	10.5492	211.1518

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 1073 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1074 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 2086 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2087 through 2096 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 2097 through 2112 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 2113 through 2152 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 2153 through 2162 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 2163 through 2221 )

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