PDB-3w5y: MamM-CTD

ID or keywords:

Entry

Database: PDB / ID: 3w5y

Title

MamM-CTD

Components

Magnetosome protein MamM

Keywords

METAL TRANSPORT / cation diffusion facilitator (CDF) / METAL ION TRANSPORT

Function / homology

Function and homology information

magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Magnetospirillum gryphiswaldense (magnetotactic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Zeytuni, N. / Davidov, G. / Zarivach, R.

Citation

Journal: Plos One / Year: 2014
Title: Cation diffusion facilitators transport initiation and regulation is mediated by cation induced conformational changes of the cytoplasmic domain
Authors: Zeytuni, N. / Uebe, R. / Maes, M. / Davidov, G. / Baram, M. / Raschdorf, O. / Nadav-Tsubery, M. / Kolusheva, S. / Bitton, R. / Goobes, G. / Friedler, A. / Miller, Y. / Schuler, D. / Zarivach, R.

History

Deposition	Feb 10, 2013	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3w5y.cif.gz	85.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3w5y.ent.gz	66.6 KB	Display	PDB format
PDBx/mmJSON format	3w5y.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/w5/3w5y ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5y	HTTPS FTP

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Related structure data

Related structure data	3w5xSC 3w5zC 3w60C 3w61C 3w62C 3w63C 3w64C 3w65C 3w66C 3w8pC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3w64-2 3w64-1 3w66-1 3qoo-d 2g3k-10 4rne-d 5dfk-d 6cte-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

Deposited unit

A: Magnetosome protein MamM

B: Magnetosome protein MamM

hetero molecules

24.1 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)	133.384, 133.384, 133.384
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	196
Space group name H-M	F23

#1: Protein	Magnetosome protein MamM / Magnetosome protein MamM / Cation efflux protein family / MamM protein Mass: 11910.398 Da / Num. of mol.: 2 / Fragment: UNP residues 215-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Strain: MSR-1 / Gene: mamM, mgI491, MGR_4095 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.08 Å³/Da / Density % sol: 40.74 % / Mosaicity: 0.332 °
Crystal grow	Method: vapor diffusion, sitting drop / pH: 8 Details: 7.5% 2-propanol 1.75M AmSO4 , pH 8, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.939 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.939 Å / Relative weight: 1

Reflection

Resolution: 1.95→20 Å / Num. obs: 13839 / % possible obs: 96.1 % / Redundancy: 5.6 % / R_merge(I) obs: 0.062 / Χ²: 2.754 / Net I/σ(I): 20.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.95-1.98	6.1	0.434	705	1.983	1	100
1.98-2.02	6.4	0.302	698	1.947	1	100
2.02-2.06	5	0.31	732	2.328	1	99.2
2.06-2.1	3.7	0.234	659	2.973	1	94.4
2.1-2.15	6	0.176	735	2.247	1	100
2.15-2.2	6.5	0.145	697	2.068	1	99.9
2.2-2.25	4.8	0.146	674	2.595	1	94.5
2.25-2.31	5.3	0.118	701	2.327	1	97.6
2.31-2.38	6.6	0.1	717	2.151	1	100
2.38-2.46	6.7	0.086	707	2.255	1	100
2.46-2.54	6.5	0.072	728	2.366	1	100
2.54-2.65	5.9	0.069	702	2.633	1	100
2.65-2.77	5	0.067	730	3.106	1	98.9
2.77-2.91	6.4	0.06	713	3.356	1	100
2.91-3.09	6.2	0.061	723	3.832	1	100
3.09-3.33	5.8	0.054	724	4.19	1	99.7
3.33-3.66	3.4	0.05	636	4.287	1	89.3
3.66-4.19	3.8	0.047	542	3.974	1	74.1
4.19-5.26	5.4	0.041	686	3.213	1	92.1
5.26-20	5.7	0.043	630	3.193	1	83.1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x

Resolution: 1.95→18.68 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.911 / WR_factor R_free: 0.2646 / WR_factor R_work: 0.2057 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7669 / SU B: 8.742 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1777 / SU R_free: 0.1759 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2687	694	5 %	RANDOM
R_work	0.2066	-	-	-
obs	0.2096	13785	95.59 %	-

Solvent computation

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

Displacement parameters

B_iso max: 112.6 Å² / B_iso mean: 37.9604 Å² / B_iso min: 17.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→18.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1242	0	15	102	1359

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.021	1293
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	862
X-RAY DIFFRACTION	r_angle_refined_deg	1.863	1.935	1755
X-RAY DIFFRACTION	r_angle_other_deg	0.979	3	2086
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.793	5	162
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.864	23.433	67
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.167	15	222
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.684	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	197
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1455
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	258
X-RAY DIFFRACTION	r_mcbond_it	1.132	1.5	801
X-RAY DIFFRACTION	r_mcbond_other	0.367	1.5	327
X-RAY DIFFRACTION	r_mcangle_it	1.86	2	1292
X-RAY DIFFRACTION	r_scbond_it	3.069	3	492
X-RAY DIFFRACTION	r_scangle_it	4.87	4.5	462

LS refinement shell

Resolution: 1.952→2.003 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	48	-
R_work	0.261	1015	-
all	-	1063	-
obs	-	-	98.88 %

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	30.7387	5.7767	-15.8103	1.0371	-5.6495	3.9002	-0.5539	1.0408	0.207	-0.3613	0.6999	0.8259	0.6447	-1.2266	-0.146	0.0833	-0.1658	-0.0519	0.4674	-0.1462	0.7667	-16.2248	-19.5247	34.1997
2	4.0354	0.0904	1.0241	3.0157	-0.2762	0.4007	0.0376	0.1914	0.1354	0.063	0.0719	0.1622	-0.0966	-0.1659	-0.1095	0.1552	0.0289	0.0388	0.1645	-0.0144	0.1879	-8.693	-15.4834	34.3335
3	3.7058	4.1275	-0.3006	4.155	-2.8593	7.5312	0.1512	-0.2576	0.5686	0.2709	-0.1585	0.365	-0.5965	-0.181	0.0073	0.1737	0.026	0.0434	0.0984	-0.0251	0.2469	-1.3794	-11.3132	30.284
4	6.44	1.2193	-2.7751	0.8378	-2.2286	4.3126	0.0811	0.4287	0.0105	-0.1375	0.2209	0.2286	0.1305	-0.3586	-0.302	0.1893	0.0036	-0.0182	0.1586	0.0061	0.1944	-6.6171	-18.2585	23.5942
5	6.4526	-4.2853	-1.7801	5.5672	0.5302	5.7221	0.0813	0.2248	0.0263	-0.2417	0.3924	0.6455	0.3649	-0.8872	-0.4737	0.1075	-0.0794	-0.0186	0.2238	0.006	0.3164	-13.7056	-29.5667	34.1866
6	6.049	-2.1707	2.3761	4.3753	2.4258	2.8574	0.0863	-0.5038	-0.0894	0.4365	-0.1862	0.2444	0.365	-0.4747	0.0999	0.1542	-0.0472	0.0513	0.1762	-0.0252	0.1844	-9.9935	-30.4921	38.3037
7	5.8409	4.132	-6.2874	5.6441	-8.0391	10.974	0.1195	-0.0072	-0.0432	0.0566	-0.0263	0.121	-0.0476	-0.1266	-0.0932	0.1755	0.0064	0.0144	0.1633	-0.0281	0.1658	-3.1923	-21.1572	25.0009
8	2.4886	-3.6065	1.7802	7.964	-2.6191	3.9749	0.0606	0.3163	0.2811	-0.355	-0.1583	-0.0215	-0.0624	-0.0525	0.0977	0.1394	-0.0117	0.0525	0.1599	0.0052	0.1886	7.7383	-15.6548	18.6844
9	9.3721	6.068	-3.9184	1.6513	-2.0321	8.3978	0.1038	-0.2234	-0.1242	0.136	-0.0818	-0.1769	-0.0242	0.6781	-0.022	0.1776	0.0165	-0.1	0.1507	-0.0218	0.4145	9.3811	-19.6651	26.9041
10	2.4094	0.4149	-2.1818	1.4349	0.166	4.5359	-0.1743	-0.0277	-0.1782	0.1141	0.0274	-0.0978	0.2932	0.0234	0.1469	0.1458	0.0125	0.025	0.1302	0.0001	0.1601	1.0757	-19.7509	34.377
11	0.5438	1.378	0.7159	8.181	-2.051	6.2423	0.1525	-0.1139	-0.0694	0.4624	-0.4124	0.0089	0.1057	-0.1857	0.2599	0.1373	-0.0012	0.0466	0.1551	-0.0103	0.1997	-7.5423	-21.0514	41.7727
12	4.8763	1.1282	-7.6662	2.7471	-5.6644	20.696	-0.1589	-0.0447	-0.2773	-0.1419	0.0194	-0.21	0.6382	-0.0783	0.1395	0.1487	-0.0055	0.0143	0.1355	-0.0159	0.1864	-2.4371	-26.6226	31.5298
13	13.4531	0.4576	1.3787	-5.2689	-1.2983	4.5369	0.0319	0.5166	0.9396	-0.006	0.2477	0.1614	-0.4354	-0.5784	-0.2796	0.2411	0.0499	-0.0046	0.1631	0.1359	0.3931	-1.8504	-14.3019	17.1635
14	29.9082	3.7809	7.6467	36.7198	4.5342	-4.262	1.6489	-0.7204	-3.6324	0.9739	-0.6954	-1.2572	0.6307	-0.7155	-0.9535	0.5184	-0.3351	0.0534	0.0465	-0.074	0.7717	0.555	-49.4656	14.1026
15	2.2517	1.4555	-0.067	5.0441	-0.3501	6.1434	-0.1789	0.1333	-0.8426	0.159	0.2133	-0.5815	0.604	0.1921	-0.0344	0.1282	0.0225	0.0384	0.1209	-0.0503	0.3041	7.6689	-42.3094	11.4512
16	11.747	3.1253	1.9492	4.1079	-2.8524	2.9301	-0.037	0.3564	-0.3546	-0.137	0.0055	-0.1153	0.2069	0.305	0.0314	0.1885	0.0667	0.0467	0.2171	-0.0087	0.1984	13.0602	-33.3073	11.6643
17	14.7291	7.4127	-1.5454	8.9136	-2.4253	0.3019	0.3013	-1.0257	-0.2194	0.223	-0.277	-0.1602	-0.0321	-0.0749	-0.0243	0.1437	0.0058	-0.0476	0.2131	0.035	0.1639	2.7194	-38.1685	20.8825
18	16.9817	-0.3144	2.7274	6.5355	-9.6116	9.6951	0.1407	0.5757	-1.4548	-0.7483	0.2042	-0.0028	1.0341	-0.3995	-0.3449	0.2012	-0.1371	-0.0383	0.2725	-0.082	0.2378	-9.0316	-44.8818	13.2658
19	26.8987	10.5779	13.2195	4.1042	5.7831	7.4611	0.0875	-0.0897	0.3083	0.0309	-0.0844	0.0465	-0.0007	-0.1532	-0.0031	0.1273	0.0164	-0.0199	0.1605	0.0356	0.175	-2.7387	-36.4549	16.457
20	6.6781	4.2509	0.1693	13.4111	2.8208	2.2113	0.1257	0.0022	0.0911	0.1765	0.1165	-0.2771	-0.0701	0.1932	-0.2422	0.1453	0.0075	0.009	0.1545	-0.0128	0.1358	12.9517	-26.1264	18.9231
21	0.1207	0.427	-1.07	1.3864	4.3844	11.2864	-0.0318	0.1731	-0.0049	-0.0505	0.1336	-0.0526	-0.2109	-0.0296	-0.1018	0.1286	0.0032	0.0324	0.1734	0.008	0.184	8.4786	-20.0862	13.9102
22	3.782	1.8081	1.2638	10.6435	6.176	1.6235	-0.0532	0.4513	0.6529	-0.6391	-0.1326	0.3516	-0.3134	-0.0449	0.1859	0.1658	0.0321	0.0128	0.2688	0.0838	0.2289	4.7833	-25.565	10.4342
23	9.3953	4.6191	-5.3836	3.9653	-2.4344	3.3665	-0.2237	0.595	0.1662	-0.2106	0.2703	0.4482	0.2047	-0.3597	-0.0466	0.1349	-0.03	-0.0194	0.1923	-0.022	0.1455	2.6048	-34.4204	7.2917
24	5.8166	-4.7062	-2.0755	5.1776	-0.1663	8.3223	0.1307	0.4367	-0.18	-0.452	-0.0345	-0.0477	1.0828	0.1081	-0.0962	0.295	-0.1189	0.0864	0.3241	-0.1738	0.2046	-1.016	-42.9742	5.1017
25	35.4624	20.2589	13.4079	13.1954	7.1585	3.5822	-0.7299	-0.2115	0.1311	-1.1369	0.4933	0.4376	-0.4743	-0.1074	0.2365	0.2741	-0.0931	-0.118	0.2805	0.071	0.2562	-4.136	-34.8027	12.1569
26	18.2921	10.979	4.9426	6.533	3.2635	8.66	0.6998	-0.8224	-1.3389	0.5284	-0.3662	-0.6604	0.0452	0.1956	-0.3336	0.1134	0.0603	-0.0296	0.3088	0.1547	0.2659	10.6883	-29.5983	22.0222

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	214 - 219
2	X-RAY DIFFRACTION	2	A	220 - 225
3	X-RAY DIFFRACTION	3	A	226 - 231
4	X-RAY DIFFRACTION	4	A	232 - 237
5	X-RAY DIFFRACTION	5	A	238 - 243
6	X-RAY DIFFRACTION	6	A	244 - 248
7	X-RAY DIFFRACTION	7	A	249 - 254
8	X-RAY DIFFRACTION	8	A	255 - 260
9	X-RAY DIFFRACTION	9	A	261 - 265
10	X-RAY DIFFRACTION	10	A	266 - 276
11	X-RAY DIFFRACTION	11	A	277 - 281
12	X-RAY DIFFRACTION	12	A	282 - 288
13	X-RAY DIFFRACTION	13	A	289 - 293
14	X-RAY DIFFRACTION	14	B	213 - 218
15	X-RAY DIFFRACTION	15	B	219 - 226
16	X-RAY DIFFRACTION	16	B	227 - 233
17	X-RAY DIFFRACTION	17	B	234 - 238
18	X-RAY DIFFRACTION	18	B	239 - 246
19	X-RAY DIFFRACTION	19	B	247 - 251
20	X-RAY DIFFRACTION	20	B	252 - 257
21	X-RAY DIFFRACTION	21	B	258 - 263
22	X-RAY DIFFRACTION	22	B	264 - 268
23	X-RAY DIFFRACTION	23	B	269 - 275
24	X-RAY DIFFRACTION	24	B	276 - 281
25	X-RAY DIFFRACTION	25	B	282 - 286
26	X-RAY DIFFRACTION	26	B	287 - 292

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi