PDB-3as5: MamA AMB-1 P212121

ID or keywords:

Entry

Database: PDB / ID: 3as5

Title

MamA AMB-1 P212121

Components

MamA

Keywords

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

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 /

SAD / 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	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	3as5.cif.gz	165.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3as5.ent.gz	132.2 KB	Display	PDB format
PDBx/mmJSON format	3as5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3as5_validation.pdf.gz	434.9 KB	Display	wwPDB validaton report
Full document	3as5_full_validation.pdf.gz	438 KB	Display
Data in XML	3as5_validation.xml.gz	18 KB	Display
Data in CIF	3as5_validation.cif.gz	26.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3as5 ftp://data.pdbj.org/pub/pdb/validation_reports/as/3as5	HTTPS FTP

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Related structure data

Related structure data	3as4C 3as8C 3asdC 3asfC 3asgC 3ashC C: citing same article (ref.)
Similar structure data	3asg-1 4xzf-1 3l0r-d 3bvo-1 2c0e-1 6h7e-1 1bfv-4 5iw3-d 5tut-d 1y2g-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: MamA

B: MamA

hetero molecules

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

1

A: MamA

hetero molecules

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

2

B: MamA

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

Unit cell

Length a, b, c (Å)	44.750, 76.194, 105.057
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	MamA / Tetratricopeptide-repeat protein Mass: 20624.461 Da / Num. of mol.: 2 / 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.34 % / Mosaicity: 1.016 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris, MgCl, PEG 3350, NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	ESRF	ID14-2		1	0.933
ROTATING ANODE			RIGAKU	2	1.5417

Detector

Type	ID	Detector	Date
ADSC QUANTUM 4	1	CCD	Jul 11, 2009
MAR scanner 345 mm plate	2	IMAGE PLATE	Oct 10, 2009

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID	Monochromator
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1	PHASING

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.933	1
2	1.5417	1

Reflection

Redundancy: 3.8 % / Av σ(I) over netI: 47.12 / Number: 87768 / R_merge(I) obs: 0.089 / Χ²: 1.34 / D res high: 2.45 Å / D res low: 20 Å / Num. obs: 23284 / % possible obs: 99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.57	20	99.9	1	0.043	2.051	3.8
5.25	6.57	100	1	0.063	1.332	4
4.6	5.25	100	1	0.05	1.284	4
4.18	4.6	100	1	0.048	1.342	4
3.88	4.18	100	1	0.054	1.384	4
3.65	3.88	100	1	0.065	1.395	4
3.47	3.65	100	1	0.078	1.285	4
3.32	3.47	100	1	0.09	1.356	4
3.19	3.32	100	1	0.111	1.348	4
3.08	3.19	100	1	0.124	1.275	4
2.99	3.08	100	1	0.141	1.206	3.9
2.9	2.99	100	1	0.173	1.257	3.9
2.83	2.9	100	1	0.206	1.297	3.9
2.76	2.83	100	1	0.225	1.241	3.8
2.7	2.76	100	1	0.255	1.296	3.7
2.64	2.7	99.7	1	0.29	1.229	3.6
2.59	2.64	99.6	1	0.312	1.235	3.4
2.54	2.59	99.1	1	0.318	1.269	3.3
2.49	2.54	98.1	1	0.338	1.329	3.1
2.45	2.49	94.7	1	0.364	1.274	2.8

Reflection

Resolution: 2→25 Å / Num. all: 25013 / Num. obs: 24938 / % possible obs: 99.7 % / Redundancy: 6.7 % / R_merge(I) obs: 0.063 / Χ²: 2.455 / Net I/σ(I): 17.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2-2.03	6.8	0.259	1241	1.522	1,2	99.8
2.03-2.07	6.8	0.227	1217	1.55	1,2	100
2.07-2.11	6.8	0.188	1242	1.682	1,2	99.9
2.11-2.15	6.8	0.168	1222	1.705	1,2	100
2.15-2.2	6.7	0.191	1211	2.035	1,2	100
2.2-2.25	6.7	0.15	1242	2.874	1,2	99.8
2.25-2.31	6.6	0.154	1226	2.679	1,2	99.7
2.31-2.37	6.8	0.12	1232	2.133	1,2	99.8
2.37-2.44	6.9	0.098	1221	2.08	1,2	100
2.44-2.52	6.9	0.091	1236	2.154	1,2	100
2.52-2.61	7	0.082	1242	2.293	1,2	100
2.61-2.71	7	0.076	1237	2.402	1,2	99.9
2.71-2.84	7.1	0.069	1245	2.51	1,2	99.9
2.84-2.99	7.1	0.064	1254	2.769	1,2	100
2.99-3.17	7.1	0.056	1268	2.856	1,2	100
3.17-3.42	6.9	0.054	1238	3.076	1,2	100
3.42-3.76	5.8	0.05	1222	3.17	1,2	96.4
3.76-4.3	5.9	0.046	1269	3.316	1,2	99.9
4.3-5.41	6.6	0.045	1302	3.227	1,2	99.9
5.41-25	6	0.045	1371	3.284	1,2	99.1

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Phasing

Phasing	Method: SAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→24.83 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.924 / WR_factor R_free: 0.2453 / WR_factor R_work: 0.1747 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8458 / SU B: 9.481 / SU ML: 0.119 / SU R Cruickshank DPI: 0.1879 / SU R_free: 0.1779 / Cross valid method: THROUGHOUT / ESU R Free: 0.178 / 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	0.241	1269	5.1 %	RANDOM
R_work	0.1757	-	-	-
obs	0.1791	23549	99.28 %	-

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: 120.28 Å² / B_iso mean: 31.3298 Å² / B_iso min: 11.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.68 Å²	0 Å²	0 Å²
2-	-	-0.53 Å²	0 Å²
3-	-	-	1.21 Å²

Refinement step

Cycle: LAST / Resolution: 2→24.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2746	0	1	302	3049

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	2833
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1902
X-RAY DIFFRACTION	r_angle_refined_deg	1.666	1.967	3843
X-RAY DIFFRACTION	r_angle_other_deg	1.012	3	4630
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.142	5	360
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	43.37	24	140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.856	15	480
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.335	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	432
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3215
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	587
X-RAY DIFFRACTION	r_mcbond_it	0.955	1.5	1764
X-RAY DIFFRACTION	r_mcbond_other	0.328	1.5	721
X-RAY DIFFRACTION	r_mcangle_it	1.574	2	2820
X-RAY DIFFRACTION	r_scbond_it	2.694	3	1069
X-RAY DIFFRACTION	r_scangle_it	4.143	4.5	1019

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	82	-
R_work	0.21	1741	-
all	-	1823	-
obs	-	-	98.75 %

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	3.5601	1.5441	-0.3053	7.9092	-5.5545	14.3734	0.0105	-0.488	0.0275	0.4811	0.0353	0.3728	-0.3697	-0.1107	-0.0458	0.0741	0.0316	0.0023	0.122	0.0144	0.1134	11.9301	12.4036	67.7661
2	5.9059	0.2903	0.1773	3.4354	-1.0717	5.582	0.0018	-0.1297	0.0529	0.0821	0.0208	0.2126	-0.2101	-0.1372	-0.0226	0.0845	0.0032	-0.0296	0.0518	-0.0024	0.0547	8.0031	14.4839	57.9402
3	5.1581	-0.7416	0.7384	13.4984	1.7787	3.5374	0.0935	-0.0694	0.0012	0.3821	-0.1089	0.4472	0.0652	0.0408	0.0154	0.1169	-0.0026	-0.0293	0.1349	0.0166	0.037	1.8492	19.8116	50.9849
4	6.4957	1.5779	1.298	4.937	-0.1064	5.7348	-0.0143	0.0241	-0.0602	0.0214	-0.104	-0.1876	0.0001	0.2268	0.1183	0.105	0.0174	0.0207	0.1134	0.028	0.0681	4.791	23.9499	41.9386
5	4.0919	-0.1272	0.7739	1.373	-0.1948	4.4816	-0.0445	-0.3047	0.0084	0.1347	0.0089	-0.0045	-0.2093	0.0571	0.0356	0.0725	-0.0185	-0.0049	0.0619	0.0278	0.1173	11.76	29.2632	32.4756
6	5.6752	0.0435	0.3503	3.3119	-0.7838	3.8015	0.0672	0.2426	-0.326	-0.1457	-0.0486	-0.2397	0.2176	0.3231	-0.0186	0.0693	-0.0175	0.006	0.0682	-0.0315	0.1321	16.6811	25.4178	19.4781
7	21.2924	9.4743	0.7691	9.4779	0.8016	0.2461	0.0829	0.1245	-0.8602	-0.0266	-0.0154	0.5023	0.0935	-0.2211	-0.0675	0.1898	-0.1439	-0.1153	0.2773	0.1304	0.2672	34.2294	22.006	20.9472
8	0.1838	1.1362	1.5964	8.6487	10.3148	14.2047	-0.1929	0.1047	-0.0525	-1.2829	0.1101	0.5948	-0.2664	0.8628	0.0829	1.3141	0.3112	0.1806	0.1897	-0.1095	1.4398	-8.8841	4.3633	7.7914
9	7.0293	-1.8868	0.6992	6.4735	-2.6564	10.815	0.2157	0.3924	-1.9229	-0.9191	0.1394	0.866	0.5727	-0.4431	-0.3551	0.171	-0.0603	-0.1316	0.0728	-0.0777	0.5633	-4.7441	12.1858	9.2952
10	8.738	-1.9128	3.1119	7.4914	-2.5456	5.6974	0.166	0.7745	-0.151	-0.9112	-0.13	0.0804	0.0851	0.1562	-0.036	0.1858	-0.0101	-0.002	0.1117	-0.0593	0.0634	0.0021	21.3149	8.4785
11	35.6508	-10.0696	-6.8436	7.6696	8.93	11.467	1.0437	3.0176	-0.8243	-0.3304	-1.3002	0.3432	-0.2004	-1.2478	0.2566	0.3911	-0.0265	-0.4636	0.3359	0.0637	0.5556	-12.9664	25.8199	3.4569
12	3.9866	-0.4981	-0.8785	1.2589	-0.0505	1.9563	0.0175	0.4535	-0.0809	-0.2048	0.0192	0.1528	0.0114	-0.1557	-0.0367	0.0794	-0.0187	-0.0421	0.0821	0.0171	0.0785	-9.4899	33.6292	12.5399
13	1.0833	0.6258	0.5705	1.9147	1.0385	0.9567	0.0409	-0.001	0.114	-0.0236	-0.0323	0.0893	-0.0859	-0.0778	-0.0085	0.0693	0.0158	0.0142	0.0502	0.0449	0.1039	-8.8347	43.9752	25.3882
14	3.2451	7.8231	-6.5751	18.8847	-15.8635	13.3293	0.4105	-0.0985	0.1471	0.9753	-0.1164	0.3823	-0.7994	0.1454	-0.2941	0.2813	0.0615	0.081	0.4639	0.0934	0.0603	-9.9143	38.8075	40.0935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	42 - 54
2	X-RAY DIFFRACTION	2	A	55 - 90
3	X-RAY DIFFRACTION	3	A	91 - 111
4	X-RAY DIFFRACTION	4	A	112 - 136
5	X-RAY DIFFRACTION	5	A	137 - 177
6	X-RAY DIFFRACTION	6	A	178 - 210
7	X-RAY DIFFRACTION	7	A	211 - 224
8	X-RAY DIFFRACTION	8	B	47 - 51
9	X-RAY DIFFRACTION	9	B	52 - 84
10	X-RAY DIFFRACTION	10	B	85 - 105
11	X-RAY DIFFRACTION	11	B	106 - 115
12	X-RAY DIFFRACTION	12	B	116 - 150
13	X-RAY DIFFRACTION	13	B	151 - 205
14	X-RAY DIFFRACTION	14	B	206 - 215

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