PDB-6d9w: Crystal structure of Deinococcus radiodurans MntH, an Nramp-famil...

ID or keywords:

Entry

Database: PDB / ID: 6d9w

Title

Crystal structure of Deinococcus radiodurans MntH, an Nramp-family transition metal transporter, in the inward-open apo state

Components

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

Keywords

TRANSPORT PROTEIN /

Transition metal /

proton /

secondary transporter / LeuT-fold

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 / Resolution: 3.941 Å

Authors

Gaudet, R. / Bane, L.B. / Weihofen, W.A. / Singharoy, A. / Zimanyi, C.M. / Bozzi, A.T.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	9P41GM104601	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	1R01GM120996	United States
National Science Foundation (NSF, United States)	NSF-MCA93S028	United States

Citation

Journal: Elife / Year: 2019
Title: Structures in multiple conformations reveal distinct transition metal and proton pathways in an Nramp transporter.
Authors: Bozzi, A.T. / Zimanyi, C.M. / Nicoludis, J.M. / Lee, B.K. / Zhang, C.H. / Gaudet, R.

History

Deposition	Apr 30, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6d9w.cif.gz	306.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	6d9w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9w ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9w	HTTPS FTP

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Related structure data

Related structure data	6c3iC 6d91C 5kte C: citing same article (ref.)
Similar structure data	5kte-d 3ld8-d 5u7r-2 7kgv-1 6ofi-d 4uao-d 6c08-1 4ye4-d 5tih-d 6p5m-6 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&software
Evidence: gel filtration

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 / Mutation: Q169H, K170H, 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 / 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) / 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) / 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: 1

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Sample preparation

Crystal	Density Matthews: 4.52 Å³/Da / Density % sol: 72.78 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 4.5 Details: 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	1
3	177	1

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	Aug 19, 2010
ADSC QUANTUM 315	2	CCD	Feb 24, 2011
ADSC QUANTUM 315	3	CCD	Feb 24, 2011

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
3	SINGLE WAVELENGTH	M	x-ray	3

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.139	1
2	1.139	1
3	0.97918	1

Reflection

Resolution: 3.94→46.47 Å / Num. obs: 11791 / % possible obs: 95 % / Redundancy: 16.6 % / CC_1/2: 0.99 / R_merge(I) obs: 0.171 / R_rim(I) all: 0.177 / Net I/σ(I): 6

Reflection shell

Resolution: 3.94→4.08 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 462 / CC_1/2: 0.189 / % possible all: 96

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 3.941→46.47 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.08

	R_factor	Num. reflection	% reflection
R_free	0.3088	1130	9.92 %
R_work	0.2711	-	-
obs	0.2748	11389	75.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.941→46.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5761	0	3	0	5764

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5894
X-RAY DIFFRACTION	f_angle_d	0.629	8063
X-RAY DIFFRACTION	f_dihedral_angle_d	10.504	3465
X-RAY DIFFRACTION	f_chiral_restr	0.04	966
X-RAY DIFFRACTION	f_plane_restr	0.005	1012

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	0.3173	52	0.247	501	X-RAY DIFFRACTION	30
4.1207-4.3378	0.2988	82	0.2259	741	X-RAY DIFFRACTION	45
4.3378-4.6093	0.2259	112	0.2127	1032	X-RAY DIFFRACTION	62
4.6093-4.9648	0.2847	138	0.2013	1296	X-RAY DIFFRACTION	77
4.9648-5.4637	0.2984	175	0.2275	1573	X-RAY DIFFRACTION	94
5.4637-6.2527	0.3053	187	0.2842	1660	X-RAY DIFFRACTION	99
6.2527-7.8716	0.3781	189	0.3418	1703	X-RAY DIFFRACTION	100
7.8716-46.4738	0.3479	195	0.3643	1753	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	0.9289	0.5029	1.0107	1.2377	0.8037	1.3219	0.1583	0.1021	-0.2767	-0.0001	-0.1908	0.7838	-0.5441	-0.4414	0.0305	0.2966	0.5585	-0.6257	0.9391	0.0502	-0.3078	37.5773	25.9686	-0.1169
2	1.5032	-0.2865	0.2824	1.1444	-0.3599	1.3936	-0.1475	0.5043	-0.1971	-0.3091	-0.2901	0.6974	0.0898	-0.5042	-0.4578	0.7884	0.4404	-0.5755	0.9549	0.6217	0.4971	35.9541	25.7406	-4.5779
3	0.8492	-0.1256	-0.496	1.4131	0.3432	0.3491	0.0949	-0.8709	0.6358	0.7249	-0.0918	0.3561	-0.544	-0.1255	0.0672	1.46	0.6607	-0.2019	1.4548	-0.488	0.1926	30.7764	36.3088	66.4234
4	0.7658	-0.606	-0.9074	1.4699	1.2414	1.3344	-0.5875	-1.0937	-0.2355	1.3425	0.6538	-0.2414	0.6882	0.6286	0.0637	1.3222	0.7865	0.1419	1.1117	-0.2175	0.3794	23.1336	27.8406	80.481
5	2.3372	1.1192	0.6576	3.1548	-1.3093	4.0845	-0.4018	0.0815	0.0149	0.2364	-0.0478	-0.0359	-0.4997	0.8737	0.1629	1.3507	-0.1599	0.4472	1.8258	-0.4502	0.2655	40.9822	29.4808	80.8933
6	2.7994	-0.2163	0.068	5.9567	-0.9318	7.2765	-1.3048	-0.4592	0.3806	0.9647	0.5704	0.1147	0.9094	1.6443	0.6537	1.1482	0.5478	-0.518	1.6429	-0.596	1.5955	49.861	45.2337	75.3674
7	1.0531	-0.3228	-0.3832	4.045	2.9018	2.1057	-0.4592	-0.5555	0.7042	-0.3519	0.2382	-0.265	-1.8213	0.0528	0.172	2.0714	-0.0007	0.3986	1.1194	-0.6637	0.8539	31.4142	48.8445	67.4003
8	1.5317	-0.755	-0.9407	3.1028	0.9147	0.647	-0.1842	-0.0519	0.5149	-0.4891	-0.2328	0.073	-0.8784	-0.4704	0.0874	1.3613	0.1727	0.4459	0.7895	-0.4287	0.5104	26.9012	28.0355	63.2125
9	0.3633	-0.0903	0.3106	0.3685	-0.0431	0.2254	0.0401	-0.5362	0.4144	0.4301	-0.0178	0.4542	-0.3679	-0.192	-0.0328	1.8171	0.5458	0.4265	1.7022	-1.1408	0.2793	30.1682	36.4714	60.4311
10	2.8659	0.5594	0.4683	5.4561	2.341	1.0229	-0.3199	-0.5162	0.2407	0.6219	-0.0549	0.4434	-0.0377	-0.0703	0.2997	1.6326	-0.1952	-0.0092	0.7399	-0.7344	0.7759	38.3672	42.119	72.8341
11	0.6197	-0.3807	0.1871	0.5104	-0.3046	0.1828	-0.2582	-0.8262	0.4017	0.7145	0.6113	-0.4904	0.4778	0.5364	-0.2765	1.6185	0.2285	0.0964	1.4829	-0.2093	0.719	45.139	29.4371	75.7095
12	4.5175	-0.6151	-3.3986	3.4313	1.7773	5.7839	0.6233	0.0769	0.8293	0.5065	0.181	0.6432	-0.158	-1.5935	-0.5076	1.652	0.1988	0.5355	2.1656	-0.2757	0.6165	21.8777	19.1073	80.7631
13	0.9402	-0.1437	-0.3899	0.3026	0.0881	0.1495	-0.2767	0.0657	-0.3804	0.1326	-0.0752	0.2429	-0.0987	-0.3014	-0.1162	0.62	0.2896	0.804	0.5929	-0.6757	0.2873	35.3695	14.9825	35.9921
14	0.387	0.2662	0.1404	0.6942	0.3256	0.9039	-0.3435	0.1419	-0.026	0.3693	-0.4905	1.024	-0.2768	-0.1537	-0.0915	0.0309	-0.3038	-0.8917	-0.2526	-0.739	-1.3886	44.5123	12.7194	4.6345
15	5.4639	0.4625	0.151	4.4957	-1.1728	2.9571	-0.1709	-0.5088	0.3975	0.5568	0.3658	0.0656	-1.2343	0.0453	-0.2215	0.7001	0.1032	-0.0005	0.8423	-0.123	0.4271	43.3597	35.7823	30.8552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 102 through 163 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 164 through 213 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 43 through 70 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 71 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 145 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 146 through 171 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 191 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 192 through 256 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 257 through 308 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 309 through 339 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 340 through 383 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 384 through 436 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 1 through 96 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 97 through 213 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 1 through 101 )

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