PDB-3asf: MamA MSR-1 C2

ID or keywords:

Entry

Database: PDB / ID: 3asf

Title

MamA MSR-1 C2

Components

Magnetosome protein MamA

Keywords

PROTEIN BINDING / Tetratricopeptide repeats (TPR) containing protein / TPR protein / protein-protein interactions / MamA / cytosol

Function / homology

Function and homology information

magnetosome / magnetosome assembly / magnetosome membrane / cell outer membrane / receptor-mediated virion attachment to host cell / identical protein binding
Similarity search - Function

Biological species

Magnetospirillum gryphiswaldense (magnetotactic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.39 Å

Authors

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

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Self-recognition mechanism of MamA, a magnetosome-associated TPR-containing protein, promotes complex assembly
Authors: Zeytuni, N. / Ozyamak, E. / Ben-Harush, K. / Davidov, G. / Levin, M. / Gat, Y. / Moyal, T. / Brik, A. / Komeili, A. / Zarivach, R.

History

Deposition	Dec 11, 2010	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2013	Group: Database references
Revision 1.2	Nov 1, 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	3asf.cif.gz	158.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3asf_validation.pdf.gz	449.8 KB	Display	wwPDB validaton report
Full document	3asf_full_validation.pdf.gz	460.6 KB	Display
Data in XML	3asf_validation.xml.gz	16.1 KB	Display
Data in CIF	3asf_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3asf ftp://data.pdbj.org/pub/pdb/validation_reports/as/3asf	HTTPS FTP

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Related structure data

Related structure data	3as4C 3as5SC 3as8C 3asdC 3asgC 3ashC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4law-2 5lfl-3 5lfm-4 5lfm-3 2y3h-2 6jb2-d 5nuh-1 6isk-1 2qsi-d 1s7e-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	#141 - Sep 2011 O-GlcNAc Transferase similarity (5) #230 - Feb 2019 Initiation Factor eIF4E similarity (5) #166 - Oct 2013 Proteasome similarity (3)

Deposited unit

A: Magnetosome protein MamA

B: Magnetosome protein MamA

hetero molecules

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

1

A: Magnetosome protein MamA

hetero molecules

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

2

B: Magnetosome protein MamA

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.129, 73.377, 90.224
Angle α, β, γ (deg.)	90.000, 93.700, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Magnetosome protein MamA / Magnetosome protein MamA / TPR-like Mass: 20657.445 Da / Num. of mol.: 2 / Fragment: UNP residues 41-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic) Strain: MSR-1 / Gene: mamA, mgI495, MGR_4099 / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93DY9
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.48 Å³/Da / Density % sol: 64.69 % / Mosaicity: 1.023 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Ammonium sulfat, HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-2 / Wavelength: 0.933 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2009

Radiation

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

Radiation wavelength

Wavelength: 0.933 Å / Relative weight: 1

Reflection

Resolution: 2.39→40 Å / Num. all: 25568 / Num. obs: 22523 / % possible obs: 99.8 % / Redundancy: 7.3 % / R_merge(I) obs: 0.079 / Χ²: 3.524 / Net I/σ(I): 15.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.4-2.44	7.3	0.558	1131	4.713	1	100
2.44-2.49	7.4	0.583	1141	4.919	1	99.9
2.49-2.53	7.5	0.524	1080	4.776	1	100
2.53-2.59	7.4	0.495	1147	4.678	1	100
2.59-2.64	7.5	0.444	1112	4.997	1	100
2.64-2.7	7.5	0.375	1121	4.09	1	100
2.7-2.77	7.4	0.316	1095	3.817	1	100
2.77-2.85	7.5	0.258	1156	3.283	1	100
2.85-2.93	7.5	0.19	1109	2.252	1	100
2.93-3.02	7.6	0.16	1127	2.287	1	100
3.02-3.13	7.5	0.124	1115	2.504	1	100
3.13-3.26	7.5	0.1	1119	2.503	1	100
3.26-3.41	7.4	0.079	1129	2.811	1	100
3.41-3.58	7.3	0.07	1135	2.976	1	100
3.58-3.81	7.2	0.061	1136	3.247	1	100
3.81-4.1	7.2	0.052	1126	3.276	1	100
4.1-4.52	7.1	0.047	1120	3.301	1	99.9
4.52-5.17	7	0.048	1146	3.335	1	99.9
5.17-6.51	6.7	0.05	1141	3.476	1	99.9
6.51-40	6.1	0.041	1137	3.233	1	97.3

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
DNA		data collection
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AS5

3as5

Resolution: 2.39→38.2 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.922 / WR_factor R_free: 0.277 / WR_factor R_work: 0.2453 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.7783 / SU B: 19.448 / SU ML: 0.198 / SU R Cruickshank DPI: 0.3376 / SU R_free: 0.2465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.338 / 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	0.2699	1132	5.1 %	RANDOM
R_work	0.247	-	-	-
obs	0.2482	22001	97.24 %	-
all	-	22586	-	-

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: 213.63 Å² / B_iso mean: 73.8563 Å² / B_iso min: 27.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.11 Å²	0 Å²	-1.38 Å²
2-	-	1.8 Å²	0 Å²
3-	-	-	-5.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.39→38.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2693	0	65	82	2840

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	2852
X-RAY DIFFRACTION	r_angle_refined_deg	1.374	1.977	3881
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.479	5	356
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.529	23.759	141
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.941	15	471
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.459	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	425
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2160
X-RAY DIFFRACTION	r_mcbond_it	1.136	1.5	1727
X-RAY DIFFRACTION	r_mcangle_it	2.074	2	2769
X-RAY DIFFRACTION	r_scbond_it	1.98	3	1125
X-RAY DIFFRACTION	r_scangle_it	3.407	4.5	1105

LS refinement shell

Resolution: 2.39→2.452 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.469	61	-
R_work	0.371	1432	-
all	-	1493	-
obs	-	-	90.76 %

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	19.6903	-0.2037	-15.9167	18.7597	0.0421	12.8697	-1.908	-0.1654	-1.9184	-1.9319	0.3465	-0.5409	1.513	0.1217	1.5616	0.932	-0.0591	0.0472	0.1523	-0.134	0.4384	-28.0315	-30.2605	-24.0604
2	4.8761	7.2734	1.7206	14.1432	-10.1074	49.3862	-1.1849	-0.6149	-0.1991	-2.0507	-0.5788	-0.7438	0.4672	-1.4291	1.7637	0.362	0.1796	-0.0797	0.1628	-0.204	0.6904	-31.068	-23.8987	-17.653
3	1.1015	-1.6597	-0.8002	3.947	-0.9858	4.0044	0.0801	-0.0102	-0.0858	-0.303	-0.0891	0.1833	0.3419	0.0175	0.009	0.3339	-0.015	-0.0317	0.3655	-0.0564	0.2113	-25.0672	-21.0317	-12.1896
4	8.2486	2.6743	-1.6192	1.6905	-1.5902	1.7061	0.2233	0.1467	-0.1915	-0.1193	0.1017	0.2117	0.1425	-0.0816	-0.3249	0.5002	0.1177	-0.0486	0.3329	-0.1242	0.1652	-25.0161	-18.2814	-27.2572
5	3.863	4.2913	-1.3369	5.2805	0.3102	6.823	-0.0144	0.0343	0.1041	0.0025	-0.039	0.1639	0.2245	-0.2471	0.0535	0.3362	0.1302	-0.0471	0.3044	-0.0632	0.2517	-28.9832	-14.5046	-19.7116
6	5.6921	-2.0776	1.5045	6.9281	-2.0767	1.3783	0.3141	0.2685	0.0878	-0.1997	-0.4076	-0.3537	-0.128	0.2615	0.0935	0.302	0.0681	0.0062	0.3326	-0.0326	0.1718	-21.2262	-9.2639	-19.3129
7	3.5002	0.1607	1.2036	2.3676	4.375	17.2919	0.0766	0.37	0.2742	0.3128	-0.165	0.3694	0.2567	-0.024	0.0883	0.3291	0.1191	0.0065	0.1939	-0.0303	0.2512	-33.1723	-4.8502	-20.0659
8	11.9622	3.1912	-0.5279	4.3835	-2.1884	3.9749	-0.0336	-0.2811	-0.5371	0.068	-0.3213	-0.1297	0.06	0.3151	0.355	0.3355	0.1039	0.0094	0.3117	-0.0131	0.27	-23.0615	-1.2052	-13.0309
9	11.7734	2.6104	1.0425	1.2164	-0.6356	5.3719	0.0913	0.252	-0.104	-0.187	-0.0595	0.0193	0.1375	0.2834	-0.0319	0.3357	0.0389	0.0169	0.3237	-0.0041	0.2136	-26.8592	4.7261	-15.5693
10	8.5525	3.3143	-7.2959	8.5074	-3.1655	12.5898	-0.1055	0.0667	0.2519	-0.0844	0.0676	0.1871	0.1997	-0.4772	0.0379	0.3441	0.0046	0.012	0.3198	-0.0354	0.2741	-39.8488	1.8372	-14.3913
11	6.4545	3.9836	-0.1553	3.4463	-0.0151	4.7211	0.0464	-0.0492	-0.0812	0.1045	-0.1045	-0.0034	0.1372	0.1425	0.058	0.3247	0.0545	0.0338	0.2615	-0.0073	0.2177	-32.7142	3.4329	-6.3991
12	3.9401	1.1207	-1.0444	2.2718	-0.1752	1.6691	0.0515	0.1601	0.1818	-0.0745	0.0017	0.1188	-0.3063	-0.1004	-0.0532	0.3642	-0.0009	-0.0164	0.2964	-0.0006	0.2333	-32.1974	11.9866	-4.8836
13	1.8791	0.1184	0.0886	2.3811	2.1334	2.8167	-0.0948	-0.4878	-0.0597	-0.0202	0.0858	0.043	0.0994	0.1303	0.009	0.306	0.0083	-0.0206	0.3029	0.0427	0.1881	-31.7654	6.8872	3.6337
14	1.3099	2.0333	-0.4773	4.4719	2.3641	8.0118	0.0159	-0.1088	0.0215	-0.0122	-0.1117	-0.0536	-0.3921	0.1049	0.0958	0.3397	0.003	-0.0698	0.3288	-0.0022	0.2792	-27.3899	18.4133	5.5927
15	2.347	0.4568	-3.2227	10.0034	5.9716	8.86	0.3869	-0.3065	-0.1402	0.7134	-0.7638	0.2074	-0.0399	0.0278	0.3769	0.3684	-0.0884	-0.0628	0.3402	0.0391	0.1483	-30.4888	9.2146	12.5817
16	6.7085	24.1887	-5.5348	87.494	-20.002	4.576	-0.1221	-0.0236	-1.2023	1.4352	-0.4926	-4.3216	-0.2829	0.0069	0.6147	1.3691	-0.1841	-0.0762	0.2338	0.2503	0.4949	-32.6541	0.3163	14.773
17	11.3492	-3.3325	-4.1479	1.4973	1.0165	1.5972	-0.7197	-1.6234	-0.0886	0.3755	0.8611	0.6897	0.1895	0.4827	-0.1414	0.8072	0.0309	0.0556	0.4627	0.4343	0.8807	-23.6205	33.2078	-24.6024
18	8.7991	1.493	-0.7492	0.254	-0.1117	0.7217	0.1459	-0.5008	0.2605	0.0094	-0.0962	0.0415	-0.3129	-0.1168	-0.0496	0.5856	-0.2576	-0.0374	0.3768	0.1486	0.2112	-19.6073	26.0059	-33.4976
19	8.667	0.0346	1.1871	0.9489	0.6298	4.7674	0.0221	0.4875	0.4172	0.4216	0.1886	0.5176	-0.4279	0.8902	-0.2107	0.5981	-0.2222	0.1996	0.3053	0.1125	0.4488	-22.3082	22.4246	-21.2025
20	12.7544	-4.72	-3.5398	2.3621	-1.1542	12.5842	0.3363	-0.3919	0.0436	-0.3218	0.2859	0.0883	0.3202	0.674	-0.6223	0.2314	-0.2723	0.0699	0.7141	-0.0867	0.1871	-16.7835	14.9817	-31.1063
21	7.9079	-1.4918	-3.6753	5.9176	0.5785	1.7324	-0.1363	-0.0444	-0.3174	0.1128	-0.0235	0.0846	0.0509	0.1191	0.1599	0.3453	-0.0167	-0.056	0.4402	0.0599	0.1021	-22.7182	12.2945	-22.5559
22	3.7015	-0.8702	-1.9352	1.4883	3.2604	7.8599	-0.1026	-0.0819	-0.136	-0.1431	-0.0008	0.2429	-0.1652	0.306	0.1034	0.2863	0.0096	-0.0846	0.3691	-0.0704	0.3445	-29.0599	10.7351	-29.1072
23	21.1364	7.5525	7.5188	2.769	3.0136	4.2306	0.0545	0.5776	-1.0268	0.0181	0.2278	-0.3516	0.0784	0.4472	-0.2823	0.2616	0.1946	0.0897	0.4485	-0.0488	0.1796	-20.5403	1.1705	-33.4689
24	3.3498	-0.4857	-0.7123	5.5533	-0.7648	0.2918	0.0984	-0.2678	0.1015	0.0374	-0.058	0.1217	0.0021	0.0667	-0.0404	0.3867	0.0716	-0.0151	0.3975	-0.0401	0.2719	-32.9408	4.1018	-31.2506
25	1.9166	-0.2706	-1.835	3.1937	1.7259	7.11	0.1346	0.2464	0.6513	-0.1539	-0.0337	-0.066	0.1156	0.2839	-0.1009	0.311	0.0498	-0.0079	0.3235	0.054	0.3363	-32.2003	6.3569	-40.7443
26	0.5002	2.0056	1.4849	8.4972	6.2558	4.6092	0.1122	0.1256	-0.0621	0.3184	0.2263	-0.5072	0.2404	0.169	-0.3385	0.609	0.2356	-0.0585	0.4885	-0.0256	0.26	-27.9704	-7.3333	-37.5304
27	12.182	-11.5415	15.5986	13.0198	-12.5252	22.4117	1.0968	0.0989	-0.6445	-0.8532	-0.3814	0.6935	1.5187	-0.2102	-0.7154	0.4989	0.0801	-0.0911	0.2876	-0.2043	0.1855	-34.5847	-5.0144	-42.1538
28	3.8119	-0.8749	2.6592	2.9765	1.5876	5.596	0.1678	0.4634	0.4302	-0.2936	-0.1208	0.278	-0.0173	0.4162	-0.047	0.3328	0.0732	-0.0359	0.36	0.0115	0.3074	-33.515	3.8968	-50.0976
29	3.064	5.1641	-4.827	15.5019	-12.7797	10.7781	0.322	0.39	-0.6473	-0.2579	-0.7478	-0.2231	0.058	0.3412	0.4258	0.4756	0.1597	-0.1475	0.3456	-0.2647	0.2491	-28.6164	-7.4816	-49.4507
30	13.4059	20.6516	7.7666	31.8679	12.132	5.2269	-0.0545	0.6097	-0.9748	0.1805	0.7956	-1.4514	1.191	-0.0003	-0.7411	2.0971	-0.4903	-0.4499	0.3746	-0.259	0.6083	-32.192	-14.32	-50.7759
31	0.4384	0.2912	-2.9465	0.2565	-1.3057	27.0174	-0.4461	0.4656	0.1672	-0.2508	0.5402	0.1753	3.8633	-1.4585	-0.0941	0.8686	-0.1945	-0.3074	1.0575	0.2515	0.3277	-30.4281	-6.6435	-56.8996
32	15.0294	-8.4616	-21.6024	4.7778	12.16	31.0533	0.1251	0.6612	-0.1936	-0.0909	-0.4057	0.0104	-0.2121	-0.9054	0.2806	0.3743	-0.0283	0.1069	0.8651	0.1102	0.7017	-26.2739	0.57	-60.4202

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 49
2	X-RAY DIFFRACTION	2	A	50 - 55
3	X-RAY DIFFRACTION	3	A	56 - 68
4	X-RAY DIFFRACTION	4	A	69 - 79
5	X-RAY DIFFRACTION	5	A	80 - 88
6	X-RAY DIFFRACTION	6	A	89 - 106
7	X-RAY DIFFRACTION	7	A	107 - 122
8	X-RAY DIFFRACTION	8	A	123 - 127
9	X-RAY DIFFRACTION	9	A	128 - 138
10	X-RAY DIFFRACTION	10	A	139 - 144
11	X-RAY DIFFRACTION	11	A	145 - 159
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17	X-RAY DIFFRACTION	17	B	44 - 55
18	X-RAY DIFFRACTION	18	B	56 - 68
19	X-RAY DIFFRACTION	19	B	69 - 86
20	X-RAY DIFFRACTION	20	B	87 - 97
21	X-RAY DIFFRACTION	21	B	98 - 109
22	X-RAY DIFFRACTION	22	B	110 - 124
23	X-RAY DIFFRACTION	23	B	125 - 131
24	X-RAY DIFFRACTION	24	B	132 - 142
25	X-RAY DIFFRACTION	25	B	143 - 156
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28	X-RAY DIFFRACTION	28	B	172 - 184
29	X-RAY DIFFRACTION	29	B	185 - 193
30	X-RAY DIFFRACTION	30	B	194 - 202
31	X-RAY DIFFRACTION	31	B	203 - 207
32	X-RAY DIFFRACTION	32	B	208 - 213

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