PDB-5m94: Crystal structure of Staphylococcus capitis divalent metal ion tr...

ID or keywords:

Entry

Database: PDB / ID: 5m94

Title

Crystal structure of Staphylococcus capitis divalent metal ion transporter (DMT) in complex with nanobody

Components

CAMELID ANTIBODY FRAGMENT, NANOBODY
Divalent metal cation transporter MntH

Keywords

TRANSPORT PROTEIN / Transition Metal Ion Transporter

Function / homology

Function and homology information

metal ion transmembrane transporter activity / symporter activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Staphylococcus capitis (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.101 Å

Authors

Dutzler, R. / Ehrnstorfer, I.A.

Citation

Journal: Nat. Struct. Mol. Biol. / Year: 2014
Title: Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport.
Authors: Ehrnstorfer, I.A. / Geertsma, E.R. / Pardon, E. / Steyaert, J. / Dutzler, R.

History

Deposition	Oct 31, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 21, 2016	Provider: repository / Type: Initial release
Supersession	Mar 1, 2023	ID: 4WGV
Revision 1.1	Mar 1, 2023	Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5m94.cif.gz	416.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5m94.ent.gz	351.3 KB	Display	PDB format
PDBx/mmJSON format	5m94.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5m94_validation.pdf.gz	457.3 KB	Display	wwPDB validaton report
Full document	5m94_full_validation.pdf.gz	469.6 KB	Display
Data in XML	5m94_validation.xml.gz	35.8 KB	Display
Data in CIF	5m94_validation.cif.gz	47.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m9/5m94 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m94	HTTPS FTP

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Related structure data

Related structure data	5m95C C: citing same article (ref.)
Similar structure data	5m95-2 4wgw-2 4wgw-1 5m95-1 3otd-d 4ttj-d 3f9k-11 3otb-d 3sbg-d 1jma-d Search similar-shape structures by Omokage search (details) 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Divalent metal cation transporter MntH

B: CAMELID ANTIBODY FRAGMENT, NANOBODY

C: Divalent metal cation transporter MntH

D: CAMELID ANTIBODY FRAGMENT, NANOBODY

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

1

A: Divalent metal cation transporter MntH

B: CAMELID ANTIBODY FRAGMENT, NANOBODY

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

2

C: Divalent metal cation transporter MntH

D: CAMELID ANTIBODY FRAGMENT, NANOBODY

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

Unit cell

Length a, b, c (Å)	114.350, 114.350, 257.870
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Divalent metal cation transporter MntH Mass: 45505.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus capitis (bacteria) Gene: mntH, BN1317_80025, SCAPIOD100025, SCAPIOD110024, SCAPIOD130025 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4MEX1
#2: Antibody	CAMELID ANTIBODY FRAGMENT, NANOBODY Mass: 13439.877 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.2 Å³/Da / Density % sol: 70.71 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 50 mM Hepes pH 7.4, 200 mM CaCl2 22-26 % PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 35853 / % possible obs: 99.6 % / Redundancy: 9.5 % / R_merge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shell	Resolution: 3.1→3.3 Å / Redundancy: 9.5 % / R_merge(I) obs: 1.2 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.101→19.931 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65

	R_factor	Num. reflection	% reflection
R_free	0.2734	1777	4.96 %
R_work	0.2374	-	-
obs	0.2391	35853	99.39 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.101→19.931 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8048	0	0	0	8048

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8204
X-RAY DIFFRACTION	f_angle_d	0.505	11156
X-RAY DIFFRACTION	f_dihedral_angle_d	14.673	2916
X-RAY DIFFRACTION	f_chiral_restr	0.038	1358
X-RAY DIFFRACTION	f_plane_restr	0.003	1378

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 (%)
3.101-3.1841	0.4401	141	0.3573	2369	X-RAY DIFFRACTION	92
3.1841-3.2773	0.3957	147	0.3439	2569	X-RAY DIFFRACTION	100
3.2773-3.3826	0.3784	124	0.3066	2594	X-RAY DIFFRACTION	100
3.3826-3.5029	0.2979	144	0.2796	2586	X-RAY DIFFRACTION	100
3.5029-3.6424	0.3089	135	0.2719	2616	X-RAY DIFFRACTION	100
3.6424-3.807	0.2972	140	0.2593	2633	X-RAY DIFFRACTION	100
3.807-4.0062	0.2514	139	0.2464	2597	X-RAY DIFFRACTION	100
4.0062-4.2549	0.2813	120	0.2187	2638	X-RAY DIFFRACTION	100
4.2549-4.5798	0.2729	122	0.2005	2680	X-RAY DIFFRACTION	100
4.5798-5.0339	0.2273	160	0.2088	2609	X-RAY DIFFRACTION	100
5.0339-5.747	0.2886	156	0.2342	2644	X-RAY DIFFRACTION	100
5.747-7.1838	0.2811	112	0.2674	2726	X-RAY DIFFRACTION	100
7.1838-19.931	0.2427	137	0.2184	2815	X-RAY DIFFRACTION	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	0.9022	-1.8055	0.6127	1.6683	-0.3586	0.4532	0.1291	0.2922	-0.7633	0.0959	-0.1453	-0.2878	-0.0083	0.2113	-0.0062	0.693	0.1073	0.026	0.775	-0.1748	0.8484	25.3211	97.7379	-12.1034
2	2.367	0.8265	-0.4172	-0.94	0.4349	-0.6062	0.2523	-0.0667	0.143	-0.1722	0.2313	0.2491	-0.1556	-0.0519	0.0252	0.6718	0.051	0.0537	0.5817	-0.1282	0.4953	12.0339	109.9539	-6.6666
3	0.3284	-0.5781	0.2719	1.1922	-0.2239	-0.0308	0.1524	0.1035	-0.5247	0.0565	-0.0908	-0.3439	-0.019	0.0202	0	0.865	0.1072	-0.0294	0.8897	-0.0206	1.0671	23.3006	97.6578	-3.0788
4	1.0296	-0.4342	-0.3587	1.3058	0.641	0.8668	0.2707	0.2192	0.1013	0.082	-0.0807	0.0838	-0.0476	0.0835	0	0.6798	0.0924	-0.0329	0.7946	-0.1957	0.6056	12.5398	104.1029	-13.8269
5	0.3733	-0.5063	0.7779	0.4226	-1.0665	0.5429	-0.1649	0.6082	-0.6208	0.2343	0.5793	-0.9241	0.2067	0.1639	0	1.1558	0.1438	0.1205	0.9101	-0.2949	1.3104	30.0111	88.8607	-19.8377
6	-0.1413	-0.207	0.4964	-0.5128	-0.1533	-0.2372	-0.8583	-0.119	0.3015	0.6242	0.0668	-0.2117	-1.0179	-0.3758	-0	0.9071	0.1695	0.1042	0.8355	-0.0517	1.3536	-20.8777	105.4828	9.6215
7	0.1299	-0.2102	0.0783	-0.0536	0.0281	-0.1415	-0.3869	1.2158	1.3864	0.3683	-0.7564	-0.9832	-0.0314	0.7751	0	1.0187	-0.0588	-0.1468	0.9836	0.1198	1.0304	-9.1544	102.2723	11.7105
8	0.0544	0.1189	-0.067	0.2866	-0.4615	0.4055	0.0403	-0.3387	-1.9599	0.5356	-0.4989	-0.0644	-0.6948	-0.0974	0	1.0317	0.0526	0.0467	1.0187	0.0976	1.3917	-15.7679	93.4836	9.6856
9	-0.0215	0.0102	0.0195	0.1324	-0.1932	0.2385	-0.1351	0.7917	-0.4599	0.232	0.1535	0.2585	0.0003	-1.0292	0	1.1206	0.0628	0.1756	0.8195	0.0674	1.1376	-25.658	91.6302	9.3089
10	0.0163	-0.0094	0.0302	-0.0375	0.0003	-0.0197	-0.4963	-0.0534	-0.6836	-0.4897	0.7333	0.5847	1.5397	0.3134	-0	1.0453	0.1605	-0.011	0.8433	-0.1301	1.1966	-10.5198	89.875	0.7795
11	0.0966	-0.1298	0.0476	0.2828	-0.2399	0.3997	-0.9958	-0.0763	-0.6252	0.7077	0.1489	0.2559	0.3341	0.0662	0	0.8889	0.0371	0.1929	1.0065	-0.0388	1.3904	-19.0457	95.6151	-0.2608
12	0.0365	0.0486	-0.1004	0.5232	-0.0505	0.1243	0.3955	0.6924	0.6532	-0.0535	-0.3814	-0.2508	0.0058	-0.4496	-0	0.7701	0.0621	0.2371	0.9627	0.0264	0.9173	-10.1545	102.0357	5.2383
13	0.0595	-0.0893	0.0917	0.033	-0.0742	0.069	-0.0609	-0.0959	-0.4833	-0.1583	-0.8252	0.5569	-0.7752	-0.1422	-0	0.7792	0.1063	0.0669	1.3261	-0.0325	1.7865	-29.9529	100.8486	1.215
14	0.0542	0.0682	0.09	-0.067	0.1874	0.1405	0.2416	-1.011	0.8881	-0.54	0.0222	0.2567	0.8089	0.1441	-0	0.8919	0.2611	-0.0326	1.2738	-0.0112	1.2029	-15.5088	95.428	13.0469
15	0.0376	-0.0377	0.0115	0.043	-0.0077	0.0029	0.1271	-0.6428	-0.4387	-0.1554	0.1005	-0.1535	0.0202	-0.2202	-0	1.41	0.0267	-0.3216	1.4395	0.1836	0.964	2.6409	91.1492	16.5122
16	0.107	0.1084	0.1316	0.2353	0.0321	0.0228	-0.6683	-0.6075	-0.44	-0.0684	-1.4238	3.0262	-0.4289	0.2292	-0.008	1.544	0.2211	-0.0028	1.4319	-0.2393	1.297	-13.5277	93.9039	18.3465
17	0.0366	0.0006	-0.0783	0.0042	-0.0074	0.0475	-0.389	0.4667	1.5888	1.0263	-0.1049	2.7261	0.1909	-0.0011	0	0.6868	0.1673	0.0434	0.8226	-0.0902	1.2647	-30.1164	105.4463	8.1276
18	2.1996	-2.4478	0.7327	3.2365	-0.782	0.4324	0.0386	1.7257	0.267	-0.5119	-1.0944	0.4871	-0.7941	-1.1521	-0.2661	1.1077	0.2807	-0.0544	1.6782	0.4973	0.9129	-14.181	132.3861	-36.5241
19	2.5502	-0.4978	-1.7316	0.5455	0.2209	1.7798	0.2499	0.9884	-0.1164	-0.0827	-0.4456	0.1982	-0.2027	-0.3744	-0.0053	0.705	0.2501	-0.0772	1.1308	-0.1225	0.6978	-17.3155	124.0964	-25.6233
20	0.9013	1.8447	-0.5821	0.8146	1.3157	-0.5619	0.1952	0.5925	0.2908	-0.5701	0.2354	0.088	-0.9634	0.1778	0.0032	1.2866	0.6453	-0.1557	1.9461	0.2346	0.7985	-16.4123	126.22	-43.6621
21	1.6806	0.0431	-0.8395	1.7236	-0.0098	0.9645	0.3328	0.5446	0.2396	-0.2247	-0.3118	0.1723	-0.2926	-0.3279	-0.0019	0.7576	0.2693	-0.0341	0.9279	0.1166	0.6708	-11.955	129.2714	-27.661
22	0.1698	-0.01	-0.291	0.5448	-0.2848	0.4739	0.7445	-0.4924	-0.2192	-0.2775	-0.5125	0.049	0.8397	0.4678	-0	1.0443	0.0978	0.0324	1.1321	-0.0985	0.9794	-20.6942	114.1825	9.3486
23	0.1018	-0.0899	0.1494	0.082	-0.0298	-0.0323	-0.6544	0.6781	0.9321	-1.0744	-0.4517	-0.3575	-0.5888	-0.4438	-0.002	0.7648	0.2135	0.0668	0.9309	-0.1241	0.9636	-30.3849	123.1981	-3.0606
24	0.3815	0.0127	-0.037	-0.1575	-0.1299	-0.009	-0.6865	-0.5441	0.9139	0.856	0.0634	-0.3511	0.0724	-0.4053	-0.0034	1.2321	0.1917	0.0489	1.0836	-0.3051	0.9451	-21.7586	125.4523	16.3986
25	0.5749	-0.2655	-0.1572	0.1696	0.0255	0.0019	-0.0673	-0.1222	-0.4909	0.3179	0.2899	-0.0903	-0.5256	0.7627	0	0.9351	0.0405	-0.1452	0.6336	-0.091	0.815	-14.9238	127.6795	6.3465
26	0.2146	0.2648	-0.0446	0.4489	-0.1457	0.1099	0.6772	0.1118	0.9613	-0.3985	-0.578	-0.1908	1.3396	0.6289	-0	1.224	0.2067	-0.0456	1.2424	-0.1376	0.8163	-19.8794	119.0864	0.5243
27	-0.1415	-0.022	0.4774	0.0446	-0.2164	-0.0508	0.1323	0.6765	1.1984	0.3798	-0.2309	-0.154	-0.3834	-0.7134	0	1.0745	0.2381	0.0085	1.1035	-0.0487	0.9991	-18.802	120.2643	14.6547
28	0.3298	-0.1044	-0.1994	0.9019	0.4626	0.0611	-0.4066	0.2759	-0.4119	1.6094	0.8056	-0.4347	-1.412	-1.3445	0.0023	1.0796	0.1362	0.2643	1.1442	0.0276	1.2994	-33.8312	126.3875	0.9257
29	0.3098	0.1019	0.0924	0.0929	0.1204	0.1043	1.5714	-0.6812	-0.1085	2.6039	0.7657	-1.1426	-0.1485	1.5375	0.0135	1.2177	0.3481	-0.0219	1.4785	-0.0391	0.8934	-16.7348	112.2398	19.5084

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 45 through 105 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 106 through 189 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 190 through 309 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 310 through 408 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 409 through 445 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 17 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 18 through 29 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 30 through 39 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 51 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 52 through 59 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 60 through 72 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 73 through 82 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 83 through 90 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 91 through 100 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 101 through 107 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 108 through 114 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 115 through 121 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 45 through 105 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 106 through 224 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 225 through 283 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 284 through 445 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 2 through 24 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 25 through 33 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 34 through 51 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 52 through 72 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 73 through 82 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 83 through 99 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 100 through 114 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 115 through 121 )

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