PDB-3ash: MamA D159K mutant 1

ID or keywords:

Entry

Database: PDB / ID: 3ash

Title

MamA D159K mutant 1

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 / identical protein binding
Similarity search - Function

Biological species

Magnetospirillum magnetotacticum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.41 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 ...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	3ash.cif.gz	154.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3ash_validation.pdf.gz	445.7 KB	Display	wwPDB validaton report
Full document	3ash_full_validation.pdf.gz	448.7 KB	Display
Data in XML	3ash_validation.xml.gz	15.7 KB	Display
Data in CIF	3ash_validation.cif.gz	22 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3ash ftp://data.pdbj.org/pub/pdb/validation_reports/as/3ash	HTTPS FTP

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Related structure data

Related structure data	3as4C 3as5SC 3as8C 3asdC 3asfC 3asgC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3asf-2 3as4-d 2q1e-2 1r23-d 1d7h-3 3w69-d 4fho-1 4gba-2 1eym-d 3hra-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

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

1

A: MamA

hetero molecules

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

2

B: MamA

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.143, 77.477, 101.811
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: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.54 Å³/Da / Density % sol: 65.28 % / Mosaicity: 0.389 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Ammonium sulfate, Glycerol, 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: 2.4→40 Å / Num. all: 23213 / Num. obs: 22006 / % possible obs: 94.8 % / Redundancy: 8.1 % / R_merge(I) obs: 0.083 / Χ²: 1.949 / Net I/σ(I): 12.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.4-2.44	8.6	0.468	1138	1.047	1	100
2.44-2.49	8.6	0.389	1138	1.023	1	100
2.49-2.53	8.6	0.33	1144	1.067	1	100
2.53-2.59	8.6	0.302	1132	1.02	1	100
2.59-2.64	8.6	0.264	1136	1.072	1	100
2.64-2.7	8.6	0.227	1133	1.145	1	100
2.7-2.77	8.6	0.203	1156	1.195	1	100
2.77-2.85	8.6	0.164	1147	1.349	1	100
2.85-2.93	8.6	0.141	1143	1.478	1	100
2.93-3.02	8.6	0.12	1135	1.51	1	100
3.02-3.13	8.5	0.104	1168	1.855	1	100
3.13-3.26	8.5	0.088	1144	2.079	1	100
3.26-3.41	8.4	0.084	1148	2.408	1	100
3.41-3.58	7.7	0.082	959	2.73	1	82.5
3.58-3.81	5.6	0.08	445	3.492	1	38.2
3.81-4.1	6.4	0.065	951	3.634	1	80.8
4.1-4.52	7.6	0.062	1162	3.961	1	100
4.52-5.17	7.6	0.059	1187	3.532	1	99.9
5.17-6.51	7.6	0.057	1191	2.927	1	100
6.51-40	7.1	0.05	1249	3.155	1	96.4

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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: 2.41→28.67 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.939 / WR_factor R_free: 0.2129 / WR_factor R_work: 0.1846 / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8715 / SU B: 10.868 / SU ML: 0.12 / SU R Cruickshank DPI: 0.2589 / SU R_free: 0.2016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.202 / 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	0.2153	1122	5.1 %	RANDOM
R_work	0.1835	-	-	-
obs	0.1851	21883	94.2 %	-
all	-	23213	-	-

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: 116.09 Å² / B_iso mean: 41.575 Å² / B_iso min: 19.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.78 Å²	0 Å²	0 Å²
2-	-	-1.69 Å²	0 Å²
3-	-	-	0.91 Å²

Refinement step

Cycle: LAST / Resolution: 2.41→28.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2712	0	35	141	2888

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.025	0.022	2806
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1877
X-RAY DIFFRACTION	r_angle_refined_deg	1.832	1.973	3803
X-RAY DIFFRACTION	r_angle_other_deg	1.024	3	4564
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.839	5	348
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.857	24	140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.334	15	479
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.134	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	421
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3133
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	577
X-RAY DIFFRACTION	r_mcbond_it	0.966	1.5	1715
X-RAY DIFFRACTION	r_mcbond_other	0.265	1.5	701
X-RAY DIFFRACTION	r_mcangle_it	1.836	2	2744
X-RAY DIFFRACTION	r_scbond_it	3.169	3	1091
X-RAY DIFFRACTION	r_scangle_it	4.924	4.5	1056

LS refinement shell

Resolution: 2.412→2.475 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.227	95	-
R_work	0.214	1518	-
all	-	1613	-
obs	-	-	95.56 %

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	13.6942	-12.4844	5.3627	22.7058	-18.9225	19.4978	0.7231	0.6983	0.0181	-0.9505	0.2763	0.8171	0.6615	-0.8721	-0.9994	0.092	-0.0194	0.0318	0.1516	-0.002	0.1768	-13.8565	3.5215	-17.1331
2	4.5516	0.8167	-1.4976	3.1158	-1.9413	3.5663	0.0132	-0.2085	0.1109	0.3382	0.0214	0.1263	-0.0513	-0.4116	-0.0346	0.049	-0.026	0.0079	0.108	-0.0026	0.0588	-5.1032	-5.2187	-9.9223
3	13.1554	-0.8377	1.7759	5.1688	0.8611	11.2468	0.0778	0.6288	0.7034	-0.254	-0.2008	0.0605	-0.2799	-0.2338	0.1231	0.0186	0.0159	-0.0035	0.0951	0.0867	0.101	-0.6357	0.4558	-21.5391
4	2.7971	1.7298	-0.7479	1.8994	0.1149	1.4222	-0.1662	0.1914	-0.1128	-0.027	0.109	-0.088	-0.0372	-0.0578	0.0572	0.0442	-0.0128	0.0088	0.0533	0.0338	0.0713	4.7352	-8.3538	-17.0984
5	3.2261	-1.2638	0.9161	2.1137	-1.546	1.8824	-0.0806	0.1841	0.1006	0.0063	-0.0145	-0.0003	0.0113	0.067	0.0951	0.0697	-0.0057	0.0156	0.0216	0.0036	0.0626	15.3374	-5.9841	-12.7295
6	1.15	-0.8612	-0.3723	1.7298	-0.139	2.6082	-0.0741	-0.1076	-0.0042	0.0393	-0.1351	0.0248	-0.0939	0.1016	0.2092	0.0506	0.0147	0.0258	0.0569	0.0053	0.0698	20.7691	-9.0864	0.8686
7	1.1779	-1.3772	0.0874	4.4635	-2.4231	1.8944	-0.036	0.1164	0.1563	0.1112	-0.0461	-0.2635	-0.0534	-0.06	0.0821	0.0324	0.0148	-0.0062	0.0417	0.0462	0.0935	30.3162	-18.9318	6.2124
8	13.7506	0.4702	-6.9057	3.0334	-5.8215	13.8073	0.0484	-0.5235	-0.5655	0.1565	0.1979	0.2665	-0.3118	-0.1372	-0.2463	0.0515	0.0537	0.0413	0.0863	0.0615	0.0869	22.5076	-21.7433	13.3432
9	6.8976	1.2668	-4.2198	13.1592	-0.7705	12.3936	0.0328	-0.003	0.0595	-0.4047	0.0858	-0.476	-1.1662	0.0648	-0.1186	0.1487	-0.015	0.0168	0.0242	0.0021	0.1004	21.5135	32.0629	6.8156
10	3.002	-0.1409	-1.2262	2.3733	0.123	2.2588	0.0644	0.0181	-0.014	-0.0589	-0.018	-0.1223	-0.204	-0.0114	-0.0464	0.0681	0.0012	0.0489	0.008	-0.0033	0.0503	13.4572	22.2544	10.2461
11	6.48	-3.2	-2.6542	4.52	1.803	1.4189	0.1352	0.2792	-0.0902	-0.3583	-0.1816	0.1796	-0.1248	-0.0538	0.0464	0.0944	0.0044	0.0135	0.0322	-0.0115	0.0245	10.3324	12.1891	5.9058
12	8.5166	4.914	-1.6886	2.8734	-0.9821	2.8096	-0.0136	-0.2257	0.294	-0.0537	-0.0598	0.1534	-0.0796	0.119	0.0734	0.098	-0.0417	0.0146	0.093	-0.0236	0.0568	12.0246	6.8763	13.4134
13	1.132	0.8107	-0.1552	0.9192	-0.6423	3.053	-0.0372	-0.0571	0.0068	-0.0661	0.0178	0.0299	0.0503	0.0701	0.0194	0.0649	-0.0168	0.0307	0.0615	-0.0341	0.0587	9.8453	-2.4805	22.2207
14	2.4549	3.2699	-0.0928	5.49	0.6881	2.0214	0.0045	-0.1334	-0.0474	-0.1234	-0.0558	-0.0007	-0.041	-0.0207	0.0513	0.0643	-0.031	0.0474	0.0333	-0.0064	0.0664	1.2643	-10.3811	31.1548
15	7.2814	8.4964	-2.9952	30.0812	10.6157	11.1053	0.5545	-0.783	0.2977	0.8397	-0.5781	0.5704	-0.1026	0.5622	0.0236	0.095	-0.0859	0.0998	0.1066	-0.0713	0.126	-1.186	-3.9085	39.2833

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 49
2	X-RAY DIFFRACTION	2	A	50 - 70
3	X-RAY DIFFRACTION	3	A	71 - 81
4	X-RAY DIFFRACTION	4	A	82 - 106
5	X-RAY DIFFRACTION	5	A	107 - 136
6	X-RAY DIFFRACTION	6	A	137 - 184
7	X-RAY DIFFRACTION	7	A	185 - 203
8	X-RAY DIFFRACTION	8	A	204 - 212
9	X-RAY DIFFRACTION	9	B	41 - 50
10	X-RAY DIFFRACTION	10	B	51 - 91
11	X-RAY DIFFRACTION	11	B	92 - 111
12	X-RAY DIFFRACTION	12	B	112 - 127
13	X-RAY DIFFRACTION	13	B	128 - 181
14	X-RAY DIFFRACTION	14	B	182 - 204
15	X-RAY DIFFRACTION	15	B	205 - 212

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