PDB-3asg: MamA D159K mutant 2

ID or keywords:

Entry

Database: PDB / ID: 3asg

Title

MamA D159K mutant 2

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. / Levin, M. / 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 / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3asg.cif.gz	152.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3asg.ent.gz	122.3 KB	Display	PDB format
PDBx/mmJSON format	3asg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3asg_validation.pdf.gz	434.3 KB	Display	wwPDB validaton report
Full document	3asg_full_validation.pdf.gz	436.8 KB	Display
Data in XML	3asg_validation.xml.gz	15 KB	Display
Data in CIF	3asg_validation.cif.gz	20.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3asg ftp://data.pdbj.org/pub/pdb/validation_reports/as/3asg	HTTPS FTP

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Related structure data

Related structure data	3as4C 3as5SC 3as8C 3asdC 3asfC 3ashC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3as5-1 6hq2-d 4xzf-1 5lsb-1 1dkk-d 2c0e-1 1lys-d 6h7e-1 2c0g-1 5i21-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

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

1

A: MamA

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

2

B: MamA

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

Unit cell

Length a, b, c (Å)	44.570, 76.471, 104.587
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: 20638.553 Da / Num. of mol.: 2 / Fragment: UNP residues 41-217 / Mutation: D159K 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

MamA / Tetratricopeptide-repeat protein

Mass: 20638.553 Da / Num. of mol.: 2 / Fragment: UNP residues 41-217 / Mutation: D159K
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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.16 Å³/Da / Density % sol: 43.03 % / Mosaicity: 0.683 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MgCl, PEG 3350, Tris, NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.33→50 Å / Num. all: 15811 / Num. obs: 15590 / % possible obs: 98.6 % / Redundancy: 5.2 % / R_merge(I) obs: 0.123 / Χ²: 2.096 / Net I/σ(I): 8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.35-2.39	4.3	0.483	745	1.15	1	98.7
2.39-2.43	4.4	0.456	777	1.162	1	99.6
2.43-2.48	4.7	0.438	771	1.317	1	99.5
2.48-2.53	4.9	0.426	756	1.391	1	99.9
2.53-2.59	5.1	0.394	788	1.586	1	100
2.59-2.65	5.4	0.394	784	1.364	1	100
2.65-2.71	5.6	0.364	766	1.475	1	100
2.71-2.79	5.7	0.331	788	1.484	1	100
2.79-2.87	5.8	0.285	784	1.727	1	100
2.87-2.96	5.7	0.237	777	1.82	1	100
2.96-3.07	5.8	0.214	770	1.881	1	100
3.07-3.19	5.7	0.174	792	2.136	1	100
3.19-3.33	5.7	0.156	773	2.303	1	100
3.33-3.51	5.5	0.134	795	2.452	1	100
3.51-3.73	4.5	0.13	628	3.66	1	78.2
3.73-4.02	4.5	0.107	770	3.599	1	98.8
4.02-4.42	5.2	0.09	806	3.526	1	100
4.42-5.06	5.2	0.083	811	3.303	1	100
5.06-6.37	5.2	0.078	833	2.412	1	100
6.37-50	5	0.047	876	2.395	1	98.5

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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: 2.33→31.72 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.2476 / WR_factor R_work: 0.1948 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8246 / SU B: 18.402 / SU ML: 0.199 / SU R Cruickshank DPI: 0.4547 / SU R_free: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.273 / 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	0.2594	772	5 %	RANDOM
R_work	0.204	-	-	-
obs	0.2067	15530	97.89 %	-
all	-	15811	-	-

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: 142.3 Å² / B_iso mean: 41.4197 Å² / B_iso min: 16.14 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.69 Å²	0 Å²	0 Å²
2-	-	-0.33 Å²	0 Å²
3-	-	-	2.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→31.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2755	0	0	102	2857

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2816
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1902
X-RAY DIFFRACTION	r_angle_refined_deg	1.516	1.967	3813
X-RAY DIFFRACTION	r_angle_other_deg	1.129	3	4626
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.021	5	354
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.526	23.869	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.893	15	481
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.416	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	429
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3175
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	583
X-RAY DIFFRACTION	r_mcbond_it	0.938	1.5	1752
X-RAY DIFFRACTION	r_mcbond_other	0.142	1.5	717
X-RAY DIFFRACTION	r_mcangle_it	1.736	2	2799
X-RAY DIFFRACTION	r_scbond_it	2.239	3	1064
X-RAY DIFFRACTION	r_scangle_it	3.734	4.5	1012

LS refinement shell

Resolution: 2.331→2.391 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.369	47	-
R_work	0.263	977	-
all	-	1024	-
obs	-	-	89.82 %

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	0.6616	-0.3489	-0.1042	0.2906	-0.5319	3.6783	-0.0244	-0.0305	-0.02	0.0095	0.0025	-0.0391	-0.0271	0.0043	0.0219	0.1643	0.0056	-0.0002	0.203	0.0207	0.1828	13.3559	12.0877	63.1853
2	2.3401	-0.8257	-1.0315	0.3588	0.0266	2.8444	-0.0026	0.0181	-0.1356	-0.0211	0.0152	0.1145	-0.0306	-0.1664	-0.0126	0.1316	0.0065	-0.025	0.1867	0.0152	0.1973	5.0647	13.6887	59.9722
3	0.5272	-0.6599	0.5475	0.8642	-0.8964	1.8069	0.0209	0.0561	0.0198	-0.0234	-0.0687	-0.0393	-0.1292	-0.0253	0.0478	0.2078	0.018	-0.0259	0.1777	0.0217	0.1644	7.149	17.4822	54.5235
4	1.6675	0.6793	0.3665	3.7056	-0.5104	0.223	0.0499	-0.0013	0.0423	0.1237	-0.0566	0.2025	0.0244	-0.0051	0.0067	0.1907	-0.0148	-0.0124	0.1919	0.0025	0.1616	1.3406	20.1941	51.3243
5	1.8133	1.5321	0.1492	1.5063	0.2634	2.3369	-0.0618	-0.0368	0.0097	-0.0149	-0.0421	0.0227	-0.0063	0.1637	0.1039	0.1427	0.017	-0.0116	0.1939	0.0347	0.166	6.4438	26.7053	41.6801
6	5.2541	-0.0992	1.0524	1.1751	0.0499	3.3696	-0.0976	-0.1588	-0.1306	0.1118	0.0706	0.095	-0.0672	0.0741	0.0271	0.133	-0.0028	-0.0038	0.1982	0.0335	0.172	14.5888	26.4368	35.5276
7	3.4398	-0.1627	-0.5818	2.0729	0.0451	3.4983	-0.0188	0.0126	-0.1223	-0.0539	0.031	-0.0649	-0.1341	-0.2552	-0.0122	0.164	-0.0291	-0.0068	0.1629	0.0114	0.2029	3.6864	27.9208	26.9098
8	3.0923	0.724	0.4597	0.2112	-0.1872	2.2888	0.0334	-0.045	-0.024	0.0282	-0.0253	0.0123	-0.2369	0.1286	-0.0081	0.1593	-0.035	-0.004	0.1986	0.0273	0.1902	16.4838	30.6429	28.8989
9	1.1712	-0.5421	0.6126	1.3116	-0.6902	1.6842	-0.0068	0.0683	-0.1005	-0.039	-0.0095	-0.0121	-0.0427	0.047	0.0163	0.1454	-0.0198	-0.0022	0.1751	0.0048	0.2099	13.6296	25.5716	21.2047
10	4.5979	-2.1273	1.0909	4.9192	-1.3462	2.3818	0.0858	0.2153	-0.0906	-0.2515	-0.0808	-0.1052	0.0622	0.0058	-0.005	0.1593	-0.0236	0.0135	0.203	0.0041	0.1589	16.0686	28.0628	14.4807
11	7.3319	-2.5691	-0.3738	14.552	-4.7332	1.7524	0.042	-0.2232	-0.0559	-0.2093	-0.1695	-0.3458	0.0676	0.1043	0.1275	0.1058	-0.0063	-0.0028	0.1821	-0.0054	0.2308	24.0739	19.3873	18.5023
12	5.2347	3.2045	4.3157	5.8769	3.9706	4.0122	0.0322	-0.1619	-0.0277	0.166	0.01	-0.0947	0.0611	-0.1209	-0.0422	0.1362	0.0287	-0.0015	0.2137	0.0304	0.1598	37.2175	24.8638	21.2676
13	6.675	12.4095	-5.7574	23.0723	-10.7039	4.966	-1.1616	0.4156	-0.3559	-2.2375	0.8253	-0.6476	1.0362	-0.3619	0.3364	0.3571	-0.1874	-0.2023	0.177	0.1242	0.5847	-8.9973	4.9911	8.6188
14	3.4728	6.2404	2.5045	11.2236	4.4978	1.8072	0.1023	-0.1473	0.1918	0.1849	-0.2222	0.4029	0.0806	-0.1236	0.1199	0.0202	-0.062	-0.0307	0.3346	0.2123	0.3887	-8.3964	12.1365	15.8117
15	2.5879	0.4649	-3.6635	0.6902	-1.4868	6.3659	0.2789	0.0901	-0.5333	-0.1378	-0.0413	0.5595	-0.2775	-0.0776	-0.2376	0.2572	-0.0463	-0.1871	0.0279	-0.0677	0.8729	-2.2454	11.3081	8.8386
16	4.0364	0.0189	4.7128	0.0032	0.0206	5.5123	-0.0796	-0.3613	-0.1167	-0.0242	0.0938	-0.0015	-0.1883	-0.4469	-0.0141	0.3725	-0.0041	-0.0095	0.2947	-0.0129	0.3002	-9.9046	16.2781	1.8184
17	1.8954	-0.2867	2.3548	2.6587	0.5161	3.2177	0.0854	-0.0914	-0.0801	-0.1383	0.0178	0.008	0.064	-0.0975	-0.1032	0.1704	-0.0337	-0.0144	0.1902	0.0015	0.1712	-1.7623	19.0915	11.4824
18	5.9568	-2.2644	1.1304	2.6821	-0.7618	1.8607	0.1017	0.3446	-0.2977	-0.2851	-0.0849	0.1615	0.0587	-0.0347	-0.0168	0.196	-0.0152	-0.0146	0.1605	-0.0286	0.1576	-6.3407	24.672	4.2049
19	1.122	-1.5511	-1.1333	2.2288	1.6206	1.1792	-0.0291	0.0489	-0.0512	-0.0907	-0.0252	0.0798	-0.0537	-0.0156	0.0543	0.1984	-0.0282	-0.024	0.2129	0.0189	0.1867	-6.7227	29.9437	10.9888
20	1.8188	-0.7174	-0.0238	2.0167	-0.1945	1.3123	0.0696	0.1812	0.0659	-0.1856	-0.0312	-0.043	-0.0291	0.008	-0.0384	0.1829	-0.0202	-0.0111	0.1971	0.0235	0.161	-5.5633	36.3783	10.8801
21	2.6777	0.5218	0.7147	0.9635	0.6312	2.0098	0.0407	0.0911	0.0492	0.0782	-0.06	0.0149	0.0131	-0.0868	0.0193	0.1653	-0.0112	0.0034	0.1875	0.0251	0.2113	-16.5824	34.2503	18.1227
22	0.6246	0.4918	-0.2889	0.786	0.5877	1.8599	-0.0178	0.0149	0.051	-0.0739	0.0305	0.0299	-0.1125	-0.053	-0.0127	0.1871	0.0063	0.0011	0.155	0.0344	0.2018	-9.5809	43.014	20.1961
23	0.1217	0.2089	0.2768	0.5588	0.7546	1.0311	0.045	-0.0159	-0.0053	0.1131	-0.0259	-0.0418	0.1275	-0.0245	-0.0191	0.1981	0.0012	0.0053	0.1728	0.0401	0.2105	-9.8986	39.8192	29.7854
24	0.1825	0.2499	-0.0359	2.975	-1.7765	1.1449	0.0161	-0.0788	0.0897	0.0333	0.0169	0.1494	0.0138	-0.0505	-0.033	0.2052	0.0105	0.019	0.1574	-0.0005	0.2	-7.6912	46.5207	34.854

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	43 - 61
2	X-RAY DIFFRACTION	2	A	62 - 79
3	X-RAY DIFFRACTION	3	A	80 - 91
4	X-RAY DIFFRACTION	4	A	92 - 111
5	X-RAY DIFFRACTION	5	A	112 - 145
6	X-RAY DIFFRACTION	6	A	146 - 155
7	X-RAY DIFFRACTION	7	A	156 - 165
8	X-RAY DIFFRACTION	8	A	166 - 179
9	X-RAY DIFFRACTION	9	A	180 - 197
10	X-RAY DIFFRACTION	10	A	198 - 205
11	X-RAY DIFFRACTION	11	A	206 - 214
12	X-RAY DIFFRACTION	12	A	215 - 224
13	X-RAY DIFFRACTION	13	B	47 - 52
14	X-RAY DIFFRACTION	14	B	53 - 60
15	X-RAY DIFFRACTION	15	B	61 - 76
16	X-RAY DIFFRACTION	16	B	77 - 82
17	X-RAY DIFFRACTION	17	B	83 - 95
18	X-RAY DIFFRACTION	18	B	96 - 116
19	X-RAY DIFFRACTION	19	B	117 - 124
20	X-RAY DIFFRACTION	20	B	125 - 140
21	X-RAY DIFFRACTION	21	B	141 - 152
22	X-RAY DIFFRACTION	22	B	153 - 177
23	X-RAY DIFFRACTION	23	B	178 - 192
24	X-RAY DIFFRACTION	24	B	193 - 216

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi