PDB-6qfj: MamB CTD magnetosome protein [Desulfamplus magnetovallimortis BW-1]

ID or keywords:

Entry

Database: PDB / ID: 6qfj

Title

MamB CTD magnetosome protein [Desulfamplus magnetovallimortis BW-1]

Components

Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

Keywords

TRANSPORT PROTEIN / Bacterial organelle / biomineralization / cation diffusion facilitators / iron transport / magnetosome biogenesis / magnetotactic bacteria / membrane invagination / structure-function analysis.

Function / homology

Function and homology information

monoatomic cation transmembrane transporter activity / membrane
Similarity search - Function

Biological species

Desulfamplus magnetovallimortis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Zeytuni, N.Z. / Keren, N.K. / Zarivach, R.Z.

Funding support

Israel, 1items

Citation

Journal: Plos One / Year: 2020
Title: From conservation to structure, studies of magnetosome associated cation diffusion facilitators (CDF) proteins in Proteobacteria.
Authors: Keren-Khadmy, N. / Zeytuni, N. / Kutnowski, N. / Perriere, G. / Monteil, C. / Zarivach, R.

History

Deposition	Jan 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 2.0	Oct 2, 2019	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1	Aug 19, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2	May 1, 2024	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qfj.cif.gz	215.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6qfj.ent.gz	175.1 KB	Display	PDB format
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Validation report

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

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Related structure data

Similar structure data	4lpt-3 5l2h-3 3tt8-d 5l2h-1 1iv7-1 3exx-d 1g4f-d 4mli-2 2j9w-1 3gdz-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

B: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

C: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

D: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

E: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

F: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

57.6 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

defined by author
Evidence: gel filtration
9.59 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

defined by author
9.59 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

defined by author
9.59 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

defined by author
9.59 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

defined by author
9.59 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

defined by author
9.59 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.973, 47.070, 74.626
Angle α, β, γ (deg.)	74.19, 84.86, 84.21
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	GLU	GLU	A	A	188 - 269	2 - 83
2	1	HIS	HIS	GLU	GLU	B	B	188 - 269	2 - 83
1	2	HIS	HIS	GLU	GLU	A	A	188 - 269	2 - 83
2	2	HIS	HIS	GLU	GLU	C	C	188 - 269	2 - 83
1	3	GLU	GLU	GLU	GLU	A	A	190 - 269	4 - 83
2	3	GLU	GLU	GLU	GLU	D	D	190 - 269	4 - 83
1	4	GLU	GLU	GLU	GLU	A	A	190 - 269	4 - 83
2	4	GLU	GLU	GLU	GLU	E	E	190 - 269	4 - 83
1	5	GLU	GLU	GLU	GLU	A	A	190 - 269	4 - 83
2	5	GLU	GLU	GLU	GLU	F	F	190 - 269	4 - 83
1	6	HIS	HIS	LEU	LEU	B	B	188 - 270	2 - 84
2	6	HIS	HIS	LEU	LEU	C	C	188 - 270	2 - 84
1	7	GLU	GLU	GLU	GLU	B	B	190 - 269	4 - 83
2	7	GLU	GLU	GLU	GLU	D	D	190 - 269	4 - 83
1	8	GLU	GLU	GLU	GLU	B	B	190 - 269	4 - 83
2	8	GLU	GLU	GLU	GLU	E	E	190 - 269	4 - 83
1	9	GLU	GLU	GLU	GLU	B	B	190 - 269	4 - 83
2	9	GLU	GLU	GLU	GLU	F	F	190 - 269	4 - 83
1	10	GLU	GLU	GLU	GLU	C	C	190 - 269	4 - 83
2	10	GLU	GLU	GLU	GLU	D	D	190 - 269	4 - 83
1	11	GLU	GLU	GLU	GLU	C	C	190 - 269	4 - 83
2	11	GLU	GLU	GLU	GLU	E	E	190 - 269	4 - 83
1	12	GLU	GLU	GLU	GLU	C	C	190 - 269	4 - 83
2	12	GLU	GLU	GLU	GLU	F	F	190 - 269	4 - 83
1	13	GLU	GLU	LEU	LEU	D	D	190 - 270	4 - 84
2	13	GLU	GLU	LEU	LEU	E	E	190 - 270	4 - 84
1	14	GLU	GLU	LEU	LEU	D	D	190 - 270	4 - 84
2	14	GLU	GLU	LEU	LEU	F	F	190 - 270	4 - 84
1	15	GLU	GLU	LEU	LEU	E	E	190 - 270	4 - 84
2	15	GLU	GLU	LEU	LEU	F	F	190 - 270	4 - 84

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family Mass: 9594.984 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfamplus magnetovallimortis (bacteria) Gene: mamB-1, DEMABW1_80065, MTBBW1_80065 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: L0R6P9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Magnetosome membrane protein MamB, putative Co/Zn/Cd cation transporter. Cation diffusion facilitator family

Mass: 9594.984 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Desulfamplus magnetovallimortis (bacteria)
Gene: mamB-1, DEMABW1_80065, MTBBW1_80065
Production host:

Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: L0R6P9

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.8 Å³/Da / Density % sol: 56.04 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 8.6 Details: 20% PEG 3,350 0.1M Tris pH 8.6 0.2M Ammonium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.932 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 14, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.932 Å / Relative weight: 1
Reflection	Resolution: 2.13→23.91 Å / Num. obs: 3384 / % possible obs: 98.4 % / Redundancy: 3.9 % / Net I/σ(I): 23.7
Reflection shell	Resolution: 2.13→2.19 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
HKL-2000		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MamM

Resolution: 2.13→23.91 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.935 / SU B: 10.511 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23453	1683	5.1 %	RANDOM
R_work	0.19965	-	-	-
obs	0.20145	31577	96.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 63.045 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.12 Å²	0.82 Å²	0.65 Å²
2-	-	-1.66 Å²	-0.73 Å²
3-	-	-	3.2 Å²

Refinement step

Cycle: 1 / Resolution: 2.13→23.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3960	0	0	156	4116

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	4029
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	4083
X-RAY DIFFRACTION	r_angle_refined_deg	1.838	1.997	5457
X-RAY DIFFRACTION	r_angle_other_deg	1.923	3	9448
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.041	5	495
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.599	25.968	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.016	15	808
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.2	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	671
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	4404
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	750
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.29	3.721	1977
X-RAY DIFFRACTION	r_mcbond_other	3.283	3.721	1976
X-RAY DIFFRACTION	r_mcangle_it	4.912	5.557	2464
X-RAY DIFFRACTION	r_mcangle_other	4.913	5.557	2465
X-RAY DIFFRACTION	r_scbond_it	4.279	4.304	2052
X-RAY DIFFRACTION	r_scbond_other	4.278	4.304	2052
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.698	6.229	2990
X-RAY DIFFRACTION	r_long_range_B_refined	10.304	35.772	15856
X-RAY DIFFRACTION	r_long_range_B_other	10.291	35.742	15732
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	5043	0.1
1	2	B	5043	0.1
2	1	A	4828	0.15
2	2	C	4828	0.15
3	1	A	4829	0.14
3	2	D	4829	0.14
4	1	A	4635	0.16
4	2	E	4635	0.16
5	1	A	4646	0.15
5	2	F	4646	0.15
6	1	B	4884	0.15
6	2	C	4884	0.15
7	1	B	4724	0.14
7	2	D	4724	0.14
8	1	B	4557	0.16
8	2	E	4557	0.16
9	1	B	4700	0.15
9	2	F	4700	0.15
10	1	C	4925	0.12
10	2	D	4925	0.12
11	1	C	4600	0.17
11	2	E	4600	0.17
12	1	C	4722	0.16
12	2	F	4722	0.16
13	1	D	4804	0.16
13	2	E	4804	0.16
14	1	D	4774	0.16
14	2	F	4774	0.16
15	1	E	4697	0.15
15	2	F	4697	0.15

LS refinement shell

Resolution: 2.127→2.182 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	92	-
R_work	0.261	1949	-
obs	-	-	80.04 %

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	3.2995	-2.1026	-0.6657	3.9831	0.495	0.7928	-0.1976	-0.0331	-0.263	0.4674	0.0357	0.359	0.1618	-0.0148	0.1619	0.1087	-0.0197	0.0149	0.0508	0.0013	0.1233	-13.5309	-0.7451	-15.0959
2	3.5838	-1.4139	0.6552	3.526	-0.7566	0.8826	0.0522	0.504	0.427	-0.073	-0.176	-0.2649	0.0016	0.1714	0.1238	0.0353	-0.0082	0.0067	0.0956	0.0354	0.1387	3.6695	14.9394	-25.4853
3	1.6084	0.5178	-1.8521	3.5988	-1.8064	3.7158	-0.1497	-0.6031	-0.3266	0.5057	-0.2212	-0.239	0.1202	0.6321	0.3709	0.1607	0.0317	-0.0365	0.2735	0.117	0.171	9.5457	-3.754	-1.2754
4	3.764	0.3032	-1.8122	0.7523	-1.1993	3.3335	-0.1597	0.485	-0.2699	-0.403	-0.1339	-0.1622	0.481	0.1087	0.2936	0.2652	0.0334	0.0905	0.1681	-0.0504	0.1193	4.3011	-8.2581	-38.9845
5	8.9322	0.0007	2.0743	1.857	-0.6643	1.8773	0.3787	1.4945	-1.2269	-0.472	-0.0503	-0.0191	-0.1067	0.1803	-0.3284	0.285	0.0784	-0.0569	0.4404	-0.267	0.3646	-20.3962	-20.8192	-45.0656
6	1.983	-0.1233	-0.5963	5.4161	0.8592	2.9191	-0.1739	-0.3419	-0.0507	0.9913	0.4473	-0.3685	-0.188	-0.0231	-0.2734	0.3318	0.1059	-0.0838	0.163	-0.014	0.1054	-22.1252	20.103	3.9579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	187 - 270
2	X-RAY DIFFRACTION	2	B	188 - 270
3	X-RAY DIFFRACTION	3	C	188 - 270
4	X-RAY DIFFRACTION	4	D	190 - 290
5	X-RAY DIFFRACTION	5	E	190 - 270
6	X-RAY DIFFRACTION	6	F	190 - 270

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Yorodumi