PDB-5kte: Crystal structure of Deinococcus radiodurans MntH, an Nramp-famil...

ID or keywords:

Entry

Database: PDB / ID: 5kte

Title

Crystal structure of Deinococcus radiodurans MntH, an Nramp-family transition metal transporter

Components

Divalent metal cation transporter MntH
Fab Heavy ChainFragment antigen-binding
Fab Light ChainFragment antigen-binding

Keywords

TRANSPORT PROTEIN/IMMUNE SYSTEM /

Divalent Metal /

Transporter / Nramp / LeuT fold / TRANSPORT PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

manganese ion transmembrane transporter activity / cadmium ion transmembrane transporter activity /

symporter activity / cellular response to iron ion /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

Deinococcus radiodurans (radioresistant)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.941 Å

Authors

Bane, L.B. / Gaudet, R. / Weihofen, W.A. / Singharoy, A.

Funding support

United States, 3items

Organization	Grant number	Country
March of Dimes Foundation		United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	9P41GM104601	United States
National Science Foundation (NSF, United States)	NSF-MCA93S028	United States

Citation

Journal: Structure / Year: 2016
Title: Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.
Authors: Bozzi, A.T. / Bane, L.B. / Weihofen, W.A. / Singharoy, A. / Guillen, E.R. / Ploegh, H.L. / Schulten, K. / Gaudet, R.

History

Deposition	Jul 11, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2016	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 27, 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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PDBx/mmCIF format	5kte.cif.gz	305.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5kte.ent.gz	247.9 KB	Display	PDB format
PDBx/mmJSON format	5kte.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kt/5kte ftp://data.pdbj.org/pub/pdb/validation_reports/kt/5kte	HTTPS FTP

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Related structure data

Related structure data	4wgw PDB Unreleased entryS S: Starting model for refinement
Similar structure data	6d9w-d 5tih-d 3ld8-d 6p5p-5 4r4n-5 5kx6-3 6gv1-d 4pjd-2 2nr6-1 6p5m-6 4gg6-2 6m3c-3 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

H: Fab Heavy Chain

L: Fab Light Chain

hetero molecules

91.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	113.131, 132.077, 220.995
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Divalent metal cation transporter MntH Mass: 45260.449 Da / Num. of mol.: 1 / Fragment: UNP residues 26-436 / Mutation: Q169H, K170HH, E251Y, E252Y, K253Y, R398H, R399H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: mntH, DR_1709 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9RTP8
#2: Antibody	Fab Heavy Chain / Fragment antigen-binding Mass: 22568.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma cell line / Production host: Mus musculus (house mouse)
#3: Antibody	Fab Light Chain / Fragment antigen-binding Mass: 23506.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma cell line / Production host: Mus musculus (house mouse)
#4: Chemical	ChemComp-OS / OSMIUM ION / Osmium Mass: 190.230 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Os

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	4.52	72.78
2	4.52	72.78
3	4.52	72.78

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
277	1	vapor diffusion	4.5	0.1 M sodium acetate pH 4.5, 0.05 M magnesium acetate, 24% PEG400 and 0.4-1 % beta-octylglucoside
277	2	vapor diffusion	4.5	0.1 M sodium acetate pH 4.5, 0.05 M magnesium acetate, 24% PEG400 and 0.4-1 % beta-octylglucoside
277	3	vapor diffusion	4.5	0.1 M sodium acetate pH 4.5, 0.05 M magnesium acetate, 24% PEG400 and 0.4-1 % beta-octylglucoside

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	177	1
2	177	2
3	177	3

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	24-ID-C	1	1.139
SYNCHROTRON	APS	24-ID-C	2	1.139
SYNCHROTRON	APS	24-ID-E	3	0.97918

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315	1	CCD	Feb 24, 2011
ADSC QUANTUM 315	2	CCD	Feb 24, 2011
ADSC QUANTUM 315	3	CCD	Aug 19, 2010

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.139	1
2	0.97918	1

Reflection

Resolution: 3.941→46.471 Å / Num. obs: 11791 / % possible obs: 95 % / Redundancy: 16.6 % / CC_1/2: 0.99 / R_merge(I) obs: 0.171 / Net I/σ(I): 6

Reflection shell

Resolution: 3.94→4.08 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 0.61 / CC_1/2: 0.189 / % possible all: 96

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
HKL-2000		data scaling
PHASER		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4WGW

4wgw
PDB Unreleased entry

Resolution: 3.941→46.471 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.86 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.3131	1130	9.92 %
R_work	0.2676	-	-
obs	0.2722	11388	75.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.941→46.471 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5622	0	3	0	5625

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5753
X-RAY DIFFRACTION	f_angle_d	0.74	7864
X-RAY DIFFRACTION	f_dihedral_angle_d	8.723	3384
X-RAY DIFFRACTION	f_chiral_restr	0.042	939
X-RAY DIFFRACTION	f_plane_restr	0.004	984

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 (%)
3.9414-4.1207	0.3544	52	0.2657	501	X-RAY DIFFRACTION	30
4.1207-4.3378	0.2768	82	0.2243	741	X-RAY DIFFRACTION	45
4.3378-4.6093	0.245	112	0.2147	1032	X-RAY DIFFRACTION	62
4.6093-4.9648	0.2801	138	0.1929	1296	X-RAY DIFFRACTION	77
4.9648-5.4637	0.2976	175	0.2221	1573	X-RAY DIFFRACTION	94
5.4637-6.2527	0.3126	187	0.2792	1660	X-RAY DIFFRACTION	99
6.2527-7.8716	0.3728	189	0.3381	1703	X-RAY DIFFRACTION	100
7.8716-46.4738	0.3578	195	0.3559	1752	X-RAY DIFFRACTION	98

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	1.0156	-1.0512	-1.158	1.8877	1.3785	1.3617	-0.0297	-0.5076	0.6539	0.857	0.0719	0.2292	-0.1767	-0.1352	-0.0076	1.1851	0.3364	0.0767	1.3421	-0.3894	0.5975	30.8089	36.3377	66.392
2	3.1191	-1.5087	-0.7691	4.2052	0.2766	3.4014	-0.9655	-1.0693	-0.686	1.5864	0.4642	-0.0243	0.7998	0.5064	0.4802	1.575	0.5637	0.2833	1.2467	-0.0808	0.8402	23.0803	27.972	80.4117
3	0.7291	0.5168	0.9209	0.7987	-0.085	2.5466	-0.3736	-0.321	0.1186	0.2528	-0.1334	0.2954	-0.6193	0.493	0.0038	1.3106	0.2552	0.2837	1.4047	-0.4579	0.6632	36.9658	35.313	70.4367
4	0.2592	-0.002	0.2915	0.2089	-0.0926	0.3676	-0.2727	-1.3926	0.7054	1.0612	0.2757	0.3673	-0.5251	-0.4465	-0.0531	1.2822	0.2571	0.4591	1.0931	-0.3983	1.1021	29.353	27.996	73.606
5	0.2393	0.0258	0.6027	1.7621	0.8328	1.835	0.2534	-0.4142	0.2911	0.3868	-0.0237	0.4031	-0.3739	0.252	-0.1587	1.3041	0.4281	0.2423	1.3193	-0.5276	0.8067	31.3769	36.096	58.971
6	1.8261	0.9873	0.2143	2.0645	-0.2985	1.0632	-0.0266	-0.7632	0.4305	0.4111	0.2284	-0.033	0.0216	0.5545	-0.2208	1.3702	0.0434	0.1147	0.7455	-0.3741	0.5695	42.2843	34.4666	74.3364
7	0.7634	0.8243	-0.7671	1.3188	-0.1254	3.6592	0.0773	-0.8736	0.7927	0.4264	0.2395	0.2498	-0.5568	-0.0871	-0.3921	1.3574	0.0651	0.5712	1.5985	-0.1303	0.7009	23.0216	19.2929	80.0752
8	0.4071	-0.1637	0.2395	2.3936	1.6503	3.3371	-0.1635	-0.2747	0.05	0.4208	-0.0476	0.2526	0.122	-0.2907	-0.032	0.5599	0.0749	0.1605	0.4365	-0.2399	0.5075	39.7882	9.7128	33.0262
9	4.382	-1.6359	-0.9945	2.534	0.148	0.9357	0.0227	0.504	0.0093	-0.4121	0.1813	-0.0854	0.4052	0.1716	-0.2028	0.9508	-0.12	0.1722	0.6116	-0.1454	0.3211	39.3806	19.9672	37.091
10	0.3015	0.2631	-0.227	0.2635	-0.0761	0.5451	-0.0902	-0.144	-0.0763	0.0991	0.0303	-0.0256	0.0879	-0.0384	0.021	0.6207	0.199	0.3773	0.7851	-0.1837	0.555	32.1291	15.8569	40.3881
11	3.84	-0.0412	-1.107	4.893	0.3503	5.1393	0.082	-0.0896	-0.0604	0.1957	-0.2885	0.5037	-0.2245	-0.2138	0.3304	0.5142	0.1931	0.0164	0.6769	-0.1807	0.2681	37.6898	17.8286	32.6539
12	1.8103	-0.4607	-0.3661	1.3859	2.7164	5.493	0.2755	-0.2698	-0.0728	0.1929	-0.3473	0.1807	0.1842	-0.5464	0.2949	0.2738	-0.0651	0.0366	0.7001	-0.4024	0.5527	34.2958	5.8764	16.7172
13	2.5045	1.5756	1.5838	2.0949	0.7213	2.2697	-0.3141	0.5608	0.258	-0.3385	0.1549	0.1241	-0.4588	0.1555	0.1682	0.2523	0.1374	-0.1261	0.5767	-0.0146	0.0809	43.6694	16.9344	-9.6787
14	0.3347	-0.1123	-0.1397	1.4984	-0.0794	0.763	-0.0453	-0.0482	0.0333	0.2221	-0.0676	0.164	-0.1345	0.0047	-0.1487	0.3507	0.0234	-0.184	0.081	-0.0318	0.1481	46.7121	13.5196	1.9905
15	0.5355	-0.4283	0.5266	0.687	0.005	3.5812	-0.0979	0.2466	0.1529	-0.1591	-0.0746	0.0755	-0.1031	-0.0379	-0.1666	0.2782	-0.0739	-0.2573	0.1245	0.0687	0.2081	45.4351	14.4585	-2.7113
16	0.6863	0.6232	-0.1935	2.5036	-0.4647	0.0984	-0.0118	0.0716	-0.0104	-0.1647	0.077	0.0159	0.0912	-0.0048	0.0887	0.2651	-0.06	-0.038	0.0274	-0.0742	0.1661	45.8945	4.5441	-0.1698
17	5.2813	1.3457	1.3453	3.8647	0.2015	6.5859	-0.3122	0.3868	0.3328	-0.1955	0.4032	-0.0908	-1.1713	-0.3278	-0.0905	0.8374	-0.1626	-0.0422	0.7123	-0.0792	0.3397	43.7051	36.8746	31.0509
18	0.4942	-0.1849	0.1224	1.0525	0.1534	0.4572	-0.0932	-0.0122	0.0106	0.0558	-0.0278	0.4647	-0.2788	-0.3199	0.0776	0.4638	0.4712	-0.1188	0.7502	-0.1049	0.5166	40.3394	28.043	8.9833
19	1.0892	-0.437	-1.884	2.8339	-1.7785	5.6797	-0.2904	1.0397	0.1279	-0.9772	0.052	0.7928	0.9318	-0.4309	-0.2022	1.0584	0.2769	-0.3699	0.992	0.1386	0.6243	31.9621	25.1782	-8.0536

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 43 through 70 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 113 through 214 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 215 through 260 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 261 through 310 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 311 through 383 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 384 through 428 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 1 through 25 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 26 through 44 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 45 through 82 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 83 through 107 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 108 through 120 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 121 through 136 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 137 through 169 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 170 through 194 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 195 through 213 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 1 through 75 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 76 through 174 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 175 through 213 )

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