PDB-3as4: MamA AMB-1 C2221

ID or keywords:

Entry

Database: PDB / ID: 3as4

Title

MamA AMB-1 C2221

Components

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 magnetotacticum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 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 9, 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	3as4.cif.gz	86.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3as4_validation.pdf.gz	438.7 KB	Display	wwPDB validaton report
Full document	3as4_full_validation.pdf.gz	439.3 KB	Display
Data in XML	3as4_validation.xml.gz	9.2 KB	Display
Data in CIF	3as4_validation.cif.gz	12 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3as4 ftp://data.pdbj.org/pub/pdb/validation_reports/as/3as4	HTTPS FTP

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Related structure data

Related structure data	3as5SC 3as8C 3asdC 3asfC 3asgC 3ashC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ash-1 4gba-2 4leu-d 2q1e-2 5lum-3 1q3p-d 7csz-d 3ash-2 5nim-d 3m19-1 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: MamA

hetero molecules

21.2 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)	80.776, 78.282, 95.999
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	MamA / Tetratricopeptide-repeat protein Mass: 20624.461 Da / Num. of mol.: 1 / Fragment: UNP residues 41-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnetospirillum magnetotacticum (bacteria) Strain: AMB-1 / Gene: mam22, mamA / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50224, UniProt: Q2W8Q0*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.68 Å³/Da / Density % sol: 66.57 % / Mosaicity: 0.686 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.9 Details: Ammonium sulfate, Glycerol, Tris, NaCl, pH 8.9, 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: 2.33→31.97 Å / Num. all: 13297 / Num. obs: 12885 / % possible obs: 96.9 % / Redundancy: 10.4 % / R_merge(I) obs: 0.087 / Χ²: 2.452 / Net I/σ(I): 13.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.35-2.39	10.9	0.467	655	1.966	1	100
2.39-2.43	11.1	0.382	651	1.828	1	100
2.43-2.48	11	0.355	652	1.824	1	100
2.48-2.53	11.1	0.317	641	1.842	1	100
2.53-2.59	11	0.263	664	1.949	1	100
2.59-2.65	11	0.252	645	1.959	1	100
2.65-2.71	11	0.232	668	1.907	1	100
2.71-2.79	11	0.191	645	2.014	1	100
2.79-2.87	10.9	0.162	672	2.057	1	100
2.87-2.96	11	0.149	647	2.225	1	100
2.96-3.07	10.8	0.117	657	2.453	1	100
3.07-3.19	10.7	0.099	664	2.522	1	100
3.19-3.33	10.5	0.087	667	3.029	1	100
3.33-3.51	10.3	0.081	661	3.577	1	100
3.51-3.73	9.1	0.08	356	3.832	1	53.1
3.73-4.02	7.7	0.072	590	3.505	1	88.6
4.02-4.42	10	0.064	666	3.553	1	99.7
4.42-5.06	10	0.063	681	3.493	1	100
5.06-6.36	9.9	0.063	686	2.611	1	100
6.36-31.97	8.9	0.054	717	2.306	1	97.8

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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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AS5

3as5

Resolution: 2.33→28.11 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.913 / WR_factor R_free: 0.2651 / WR_factor R_work: 0.2142 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.7616 / SU B: 17.571 / SU ML: 0.187 / SU R Cruickshank DPI: 0.2455 / SU R_free: 0.2237 / Cross valid method: THROUGHOUT / ESU R Free: 0.224 / 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	0.2704	639	5 %	RANDOM
R_work	0.2154	-	-	-
obs	0.218	12779	95.57 %	-
all	-	13297	-	-

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: 201.49 Å² / B_iso mean: 58.0209 Å² / B_iso min: 25.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.64 Å²	0 Å²	0 Å²
2-	-	-5.1 Å²	0 Å²
3-	-	-	-4.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→28.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1339	0	30	68	1437

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	1387
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	919
X-RAY DIFFRACTION	r_angle_refined_deg	1.624	1.983	1880
X-RAY DIFFRACTION	r_angle_other_deg	0.956	3	2231
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.336	5	169
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	44.922	23.824	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.999	15	232
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.345	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	207
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1534
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	285
X-RAY DIFFRACTION	r_mcbond_it	0.752	1.5	843
X-RAY DIFFRACTION	r_mcbond_other	0.202	1.5	345
X-RAY DIFFRACTION	r_mcangle_it	1.338	2	1347
X-RAY DIFFRACTION	r_scbond_it	2.145	3	544
X-RAY DIFFRACTION	r_scangle_it	3.325	4.5	533

LS refinement shell

Resolution: 2.328→2.389 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	53	-
R_work	0.289	814	-
all	-	867	-
obs	-	-	89.75 %

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	9.4342	-15.4381	4.3905	28.8874	-20.8504	54.2149	-1.7782	-0.5063	-0.5387	0.5406	-0.5918	0.0505	5.3244	2.9867	2.37	1.404	0.3051	-0.0349	0.563	0.4802	0.6752	-11.5193	-33.2366	-0.8358
2	5.5049	0.5046	1.1344	4.9423	2.0876	13.5835	0.0627	-0.3012	-0.3359	0.8143	0.0074	-0.1868	1.0196	0.1493	-0.0701	0.4066	-0.0126	-0.0617	0.0683	0.0124	0.2433	-15.932	-24.8444	-4.2742
3	10.0427	-3.1954	5.3968	5.1646	1.3141	7.7896	0.2664	0.3319	0.1395	0.2482	-0.2604	-0.0201	0.1575	-0.4868	-0.006	0.2593	-0.0131	0.0013	0.1635	-0.0214	0.1847	-19.7348	-18.5618	-8.2588
4	15.9437	-4.4634	4.7078	11.5542	5.5264	18.3986	0.2243	-0.3818	-0.1169	0.6179	-0.6123	1.0063	0.6473	-1.2188	0.3881	0.2116	-0.0669	0.0488	0.285	-0.0158	0.1726	-21.808	-13.5685	-1.8262
5	4.9017	0.5689	1.6326	1.9933	2.1713	13.0535	-0.0324	-0.3153	0.0785	0.1014	-0.0731	-0.2764	0.2955	0.6497	0.1055	0.1885	-0.0002	0.0115	0.2083	0.0607	0.2738	-11.0376	-9.8548	-3.4544
6	11.5452	-0.0735	3.6019	12.8613	-4.7055	13.1639	0.1671	0.3756	-0.1849	-0.527	-0.295	1.191	0.3853	-1.1716	0.1279	0.2257	0.0129	-0.0126	0.2615	-0.0478	0.238	-21.9429	-4.2913	-11.4639
7	5.6241	0.0698	-2.764	8.5803	0.7863	4.8247	-0.1089	-0.4384	0.3272	0.0804	0.1394	0.0169	0.0064	0.2318	-0.0306	0.1874	0.0243	-0.0239	0.2881	0.0023	0.2113	-13.3128	0.114	-7.4644
8	6.8332	-1.7706	-0.1161	4.1189	0.7795	2.1592	-0.027	-0.2287	-0.1383	0.1828	0.1299	-0.4468	-0.0354	0.3874	-0.1029	0.2408	-0.0014	0.0173	0.2931	0.0085	0.1942	-6.3044	-4.0332	-16.0569
9	5.9262	-1.8519	-2.4812	3.3328	1.791	4.8073	0.094	0.0882	0.2822	-0.2211	0.073	-0.0249	-0.3764	0.0849	-0.1669	0.2561	0.0316	-0.0048	0.2018	0.0291	0.1371	-11.7237	4.395	-19.3165
10	4.1524	1.7221	-0.0537	6.697	0.505	3.3065	0.1061	0.5294	-0.3605	-0.121	-0.13	0.0206	0.2506	0.3632	0.024	0.3675	0.1035	-0.0324	0.2682	0.0219	0.1101	-13.7625	3.7859	-27.889
11	6.3225	-4.2899	-3.1651	6.6971	-0.7279	11.7573	-0.1041	0.0572	0.1525	0.0379	-0.2504	0.1896	0.2451	0.5778	0.3545	0.2911	0.0153	-0.0192	0.2364	0.0829	0.1431	-15.1737	13.2005	-29.5499
12	32.1346	-29.9829	-8.5484	40.7406	-0.085	7.4034	0.0645	0.051	-1.6392	-0.47	-1.0592	0.681	0.3108	0.8225	0.9947	0.9852	0.2496	0.0725	0.8097	-0.0342	0.1603	-12.5735	2.0143	-37.4539

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 53
2	X-RAY DIFFRACTION	2	A	54 - 82
3	X-RAY DIFFRACTION	3	A	83 - 96
4	X-RAY DIFFRACTION	4	A	97 - 105
5	X-RAY DIFFRACTION	5	A	106 - 122
6	X-RAY DIFFRACTION	6	A	123 - 130
7	X-RAY DIFFRACTION	7	A	131 - 139
8	X-RAY DIFFRACTION	8	A	140 - 152
9	X-RAY DIFFRACTION	9	A	153 - 179
10	X-RAY DIFFRACTION	10	A	180 - 192
11	X-RAY DIFFRACTION	11	A	193 - 205
12	X-RAY DIFFRACTION	12	A	206 - 212

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