PDB-3as8: MamA MSR-1 P41212

ID or keywords:

Entry

Database: PDB / ID: 3as8

Title

MamA MSR-1 P41212

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 / identical protein binding
Similarity search - Function

Biological species

Magnetospirillum gryphiswaldense (magnetotactic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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 10, 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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PDBx/mmCIF format	3as8.cif.gz	98.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3as8_validation.pdf.gz	434.8 KB	Display	wwPDB validaton report
Full document	3as8_full_validation.pdf.gz	435.6 KB	Display
Data in XML	3as8_validation.xml.gz	11.7 KB	Display
Data in CIF	3as8_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3as8 ftp://data.pdbj.org/pub/pdb/validation_reports/as/3as8	HTTPS FTP

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Related structure data

Related structure data	3as4C 3as5SC 3asdC 3asfC 3asgC 3ashC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ou7-4 2nn4-d 2lvp-d 2dli-d 4c55-2 1mk9-1 5lfm-6 5ou7-3 1tjc-d 4c55-1 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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	58.888, 58.888, 144.092
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Magnetosome protein MamA / Magnetosome protein MamA / TPR-like Mass: 20657.445 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 238 / 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: 3.02 Å³/Da / Density % sol: 59.32 % / Mosaicity: 1.205 °
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→17 Å / Num. all: 17853 / Num. obs: 17139 / % possible obs: 96 % / Redundancy: 19 % / R_merge(I) obs: 0.092 / R_rim(I) all: 0.092 / Χ²: 2.522 / Net I/σ(I): 14.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2-2.03	19	0.725	800	1.831	1	93.6
2.03-2.07	17.8	0.587	818	2.066	1	94
2.07-2.11	18	0.474	794	2.092	1	91.3
2.11-2.15	19.7	0.399	836	1.877	1	95.1
2.15-2.2	20.3	0.317	800	1.897	1	93.6
2.2-2.25	18.1	0.29	836	2.32	1	94.9
2.25-2.31	19.1	0.249	825	2.188	1	93
2.31-2.37	20.1	0.197	806	1.901	1	93.9
2.37-2.44	20.1	0.187	840	1.966	1	94.1
2.44-2.52	19.9	0.16	822	2.137	1	94.3
2.52-2.61	19	0.148	832	2.322	1	95.3
2.61-2.71	17.6	0.137	832	2.551	1	94.9
2.71-2.84	18.5	0.118	860	2.625	1	96.4
2.84-2.98	18.5	0.095	884	2.695	1	98.3
2.98-3.17	18.5	0.086	883	3.082	1	99.1
3.17-3.41	17.4	0.077	899	3.347	1	99.4
3.41-3.75	15.7	0.071	896	3.765	1	99.4
3.75-4.29	17.2	0.062	927	3.49	1	100
4.29-5.37	22.4	0.059	949	3.107	1	100
5.37-17	22.8	0.052	1000	2.923	1	98.3

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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→14.94 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.927 / WR_factor R_free: 0.2234 / WR_factor R_work: 0.1806 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8544 / SU B: 7.722 / SU ML: 0.098 / SU R Cruickshank DPI: 0.159 / SU R_free: 0.1519 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.159 / 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	0.2251	861	5.1 %	RANDOM
R_work	0.1787	-	-	-
obs	0.181	17037	95.54 %	-
all	-	17853	-	-

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: 90.41 Å² / B_iso mean: 28.6243 Å² / B_iso min: 10.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.53 Å²	0 Å²	0 Å²
2-	-	-1.53 Å²	0 Å²
3-	-	-	3.06 Å²

Refinement step

Cycle: LAST / Resolution: 2→14.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1417	0	15	238	1670

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	1511
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1010
X-RAY DIFFRACTION	r_angle_refined_deg	1.838	1.972	2060
X-RAY DIFFRACTION	r_angle_other_deg	1.114	3	2464
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.241	5	196
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.399	24.026	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.073	15	260
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.003	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.127	0.2	231
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1713
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	312
X-RAY DIFFRACTION	r_mcbond_it	1.047	1.5	925
X-RAY DIFFRACTION	r_mcbond_other	0.362	1.5	376
X-RAY DIFFRACTION	r_mcangle_it	1.754	2	1491
X-RAY DIFFRACTION	r_scbond_it	3.142	3	586
X-RAY DIFFRACTION	r_scangle_it	4.574	4.5	562

LS refinement shell

Resolution: 2.003→2.055 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.374	71	-
R_work	0.267	1106	-
all	-	1177	-
obs	-	-	92.9 %

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	12.1731	-14.1152	1.4453	16.4914	-2.7646	20.8438	-0.8175	-0.7005	0.3358	1.2929	0.8295	-0.3431	-0.2265	-0.3297	-0.012	0.636	-0.2726	0.0631	0.3137	-0.0899	0.1322	18.2905	-2.2478	29.1592
2	1.1571	1.0882	2.3366	3.816	1.7485	4.8035	-0.128	-0.0256	0.0948	0.0145	-0.0244	0.0365	-0.2629	-0.0564	0.1525	0.0916	0.0116	0.0129	0.1035	-0.015	0.1394	15.4191	-3.4141	19.0735
3	3.2316	-0.515	-0.3951	2.1535	-0.9924	5.7163	0.059	0.0782	0.3922	-0.0647	-0.0637	0.0343	-0.2449	-0.1473	0.0047	0.1131	-0.0125	0.0111	0.0926	-0.0094	0.1025	15.6254	-9.3593	12.7841
4	10.866	-0.7329	-1.2507	3.9169	0.1456	1.8492	0.2035	-0.9172	-0.0407	0.6814	-0.1132	0.3025	0.187	-0.0752	-0.0904	0.2354	-0.0459	0.0564	0.1401	-0.0185	0.0496	12.1974	-12.3447	26.3488
5	2.2457	0.4082	-0.9411	3.1013	0.1906	3.3037	0.0034	0.0085	0.0116	0.0632	-0.0967	0.1317	0.0534	-0.16	0.0932	0.111	-0.0332	0.0099	0.0924	-0.0083	0.0737	11.5767	-16.1013	15.2499
6	6.3416	-1.1078	-3.6499	2.9468	0.9649	2.9562	-0.0588	-0.3515	-0.1884	0.1484	-0.0684	-0.2106	0.1833	0.0787	0.1272	0.1508	-0.0389	-0.0296	0.1207	0.0182	0.0506	9.8303	-22.5453	19.5053
7	6.9194	-5.0028	-0.6652	7.124	-2.3333	2.326	-0.142	-0.5342	0.089	0.4562	0.205	-0.0032	-0.2701	0.1643	-0.0629	0.1015	-0.0463	-0.0056	0.2177	-0.0315	0.092	1.568	-17.7679	25.6588
8	2.2829	0.3632	0.3215	1.1885	0.3403	1.6151	0.0386	-0.1682	-0.0115	0.0835	-0.0185	-0.0124	-0.0024	-0.0349	-0.0201	0.1005	-0.0044	-0.0227	0.0954	0.0046	0.084	-2.8494	-21.5644	14.1292
9	2.0268	0.0035	0.2438	1.4122	-0.7716	1.9467	0.0215	-0.0291	-0.0625	-0.033	-0.0239	-0.1436	0.0641	0.0209	0.0024	0.0875	-0.0045	-0.0172	0.0851	-0.0018	0.0957	-6.9776	-24.598	5.7108
10	7.477	-3.984	2.2312	6.278	-3.3898	2.1915	-0.0336	-0.5315	-0.2211	0.3063	0.0976	0.0052	0.1206	-0.2772	-0.064	0.2626	-0.1509	-0.0456	0.1962	0.023	0.0727	-12.6442	-34.3884	7.9757
11	0.8483	-1.0502	0.4267	2.227	-0.1701	3.2388	-0.0495	0.0472	0.0354	-0.1101	0.0149	-0.1133	-0.0683	-0.0964	0.0345	0.0844	0.0003	-0.0064	0.1006	-0.0028	0.0924	-13.0302	-22.1908	-0.8861
12	1.6281	2.6244	-0.8403	4.6266	-0.6064	1.9822	0.0014	-0.0495	-0.1847	0.0225	-0.0462	-0.3515	0.1664	0.0836	0.0448	0.1095	0.0033	-0.0007	0.1036	-0.0001	0.0904	-10.4092	-32.9507	-3.2111
13	2.834	0.883	-0.8131	2.9831	0.6438	2.8875	0.04	0.0705	0.0859	-0.0802	0.0057	0.0375	-0.1222	-0.1454	-0.0457	0.0836	0.0044	-0.0043	0.1115	-0.0125	0.0803	-15.2089	-33.9896	-8.3004
14	3.6921	-5.5241	-2.1317	9.236	2.8012	1.437	0.0412	0.0655	-0.086	-0.0081	0.0168	-0.0477	-0.1962	-0.1541	-0.0579	0.1881	0.0118	0.1116	0.1589	0.0547	0.2613	-8.1384	-21.5603	-15.2269
15	21.5758	16.2499	-14.3758	16.0117	-2.2206	29.2391	-0.524	0.2183	0.2757	-0.5737	0.366	0.3313	0.089	0.1002	0.158	0.3031	-0.028	0.0166	0.1977	-0.0092	0.1545	-0.819	-16.3233	-17.1085

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	42 - 46
2	X-RAY DIFFRACTION	2	A	47 - 56
3	X-RAY DIFFRACTION	3	A	57 - 69
4	X-RAY DIFFRACTION	4	A	70 - 81
5	X-RAY DIFFRACTION	5	A	82 - 95
6	X-RAY DIFFRACTION	6	A	96 - 104
7	X-RAY DIFFRACTION	7	A	105 - 111
8	X-RAY DIFFRACTION	8	A	112 - 145
9	X-RAY DIFFRACTION	9	A	146 - 160
10	X-RAY DIFFRACTION	10	A	161 - 168
11	X-RAY DIFFRACTION	11	A	169 - 182
12	X-RAY DIFFRACTION	12	A	183 - 194
13	X-RAY DIFFRACTION	13	A	195 - 211
14	X-RAY DIFFRACTION	14	A	212 - 215
15	X-RAY DIFFRACTION	15	A	216 - 222

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