PDB-3asd: MamA R50E mutant

ID or keywords:

Entry

Database: PDB / ID: 3asd

Title

MamA R50E mutant

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: 2.45 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 / 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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PDBx/mmCIF format	3asd.cif.gz	71.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3asd.ent.gz	52.8 KB	Display	PDB format
PDBx/mmJSON format	3asd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3asd_validation.pdf.gz	426.3 KB	Display	wwPDB validaton report
Full document	3asd_full_validation.pdf.gz	428.2 KB	Display
Data in XML	3asd_validation.xml.gz	7.8 KB	Display
Data in CIF	3asd_validation.cif.gz	9.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/as/3asd ftp://data.pdbj.org/pub/pdb/validation_reports/as/3asd	HTTPS FTP

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Related structure data

Related structure data	3as4C 3as5SC 3as8C 3asfC 3asgC 3ashC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6uxm-1 3kes-1 1sp0-d 1gak-d 2jm5-d 5lw2-d 3rfi-2 6am3-1 3b09-1 1hii-d 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

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	43.649, 43.649, 207.449
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22

#1: Protein	MamA / Tetratricopeptide-repeat protein Mass: 22280.137 Da / Num. of mol.: 1 / Fragment: UNP residues 41-217 / Mutation: R50E 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.: 20 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

MamA / Tetratricopeptide-repeat protein

Mass: 22280.137 Da / Num. of mol.: 1 / Fragment: UNP residues 41-217 / Mutation: R50E
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.: 20 / 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: 2.22 Å³/Da / Density % sol: 44.53 % / Mosaicity: 0.535 °
Crystal grow	Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MES, NaCl, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.972 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.972 Å / Relative weight: 1

Reflection

Resolution: 2.45→50 Å / Num. all: 8171 / Num. obs: 8008 / % possible obs: 98 % / Redundancy: 10 % / R_merge(I) obs: 0.048 / Χ²: 2.268 / Net I/σ(I): 23.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.45-2.49	10.6	0.285	378	1.549	1	100
2.49-2.54	10.9	0.293	391	1.604	1	100
2.54-2.59	10.6	0.23	413	1.617	1	100
2.59-2.64	11.4	0.206	370	1.809	1	99.7
2.64-2.7	9.4	0.226	402	2.554	1	100
2.7-2.76	10.7	0.149	390	1.91	1	100
2.76-2.83	10.7	0.114	398	1.79	1	100
2.83-2.9	11	0.094	397	1.894	1	100
2.9-2.99	10.8	0.082	388	1.96	1	99.7
2.99-3.09	10.5	0.069	410	2.173	1	100
3.09-3.2	10.5	0.057	394	2.338	1	100
3.2-3.32	10.8	0.052	403	2.249	1	100
3.32-3.48	9.2	0.05	408	2.527	1	100
3.48-3.66	10.1	0.043	415	2.529	1	100
3.66-3.89	9.1	0.038	397	2.611	1	98.8
3.89-4.19	9.3	0.04	394	2.771	1	96.6
4.19-4.61	9.2	0.04	407	3.181	1	96.4
4.61-5.28	9.1	0.039	407	3.424	1	95.5
5.28-6.65	9.7	0.039	437	3.044	1	98
6.65-50	7.1	0.031	409	2.351	1	80

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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: 2.45→42.71 Å / Cor.coef. F_o:F_c: 0.89 / Cor.coef. F_o:F_c free: 0.886 / WR_factor R_free: 0.332 / WR_factor R_work: 0.2779 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7549 / SU B: 22.491 / SU ML: 0.227 / SU R Cruickshank DPI: 0.402 / SU R_free: 0.3103 / Cross valid method: THROUGHOUT / ESU R Free: 0.31 / 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	0.325	362	4.6 %	RANDOM
R_work	0.2721	-	-	-
obs	0.2745	7946	97.86 %	-
all	-	8171	-	-

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: 109.06 Å² / B_iso mean: 56.0533 Å² / B_iso min: 30.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.26 Å²	0 Å²	0 Å²
2-	-	1.26 Å²	0 Å²
3-	-	-	-2.52 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→42.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1069	0	0	20	1089

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	1106
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	741
X-RAY DIFFRACTION	r_angle_refined_deg	1.851	1.967	1503
X-RAY DIFFRACTION	r_angle_other_deg	1.065	3	1810
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.273	5	142
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.06	24.464	56
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.167	15	187
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.455	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	171
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1255
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	225
X-RAY DIFFRACTION	r_mcbond_it	0.68	1.5	688
X-RAY DIFFRACTION	r_mcbond_other	0.159	1.5	281
X-RAY DIFFRACTION	r_mcangle_it	1.257	2	1104
X-RAY DIFFRACTION	r_scbond_it	2.025	3	418
X-RAY DIFFRACTION	r_scangle_it	3.236	4.5	396

LS refinement shell

Resolution: 2.446→2.509 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.44	26	-
R_work	0.462	532	-
all	-	558	-
obs	-	-	98.76 %

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	0.3141	0.7413	1.6979	1.7651	4.0265	9.2027	-0.1113	0.0452	-0.0053	-0.2544	0.1856	-0.0565	-0.6507	0.3416	-0.0743	0.4079	-0.1109	-0.0477	0.8176	-0.207	0.5215	-16.4862	32.6615	8.8383
2	9.3519	5.4147	-4.4549	3.2245	-2.7099	2.3856	0.0927	-0.0074	0.495	0.0724	-0.1478	0.0864	-0.282	0.2657	0.0551	0.5758	-0.0768	-0.0225	0.5837	0.1932	0.5957	-17.0483	32.8798	-4.162
3	12.1301	-0.5529	-0.3676	1.5762	1.4952	1.629	0.1232	-0.3024	0.7538	-0.0673	0.0071	-0.4066	-0.3032	0.1248	-0.1303	0.4022	-0.1627	-0.1153	0.6161	-0.0456	0.6011	-10.2221	30.2872	3.5133
4	4.6212	0.2188	-1.293	4.4266	0.9649	5.2725	0.2731	-0.0057	0.1154	-0.0682	-0.2008	0.3646	0.2493	-0.4562	-0.0723	0.0503	0.0174	-0.0051	0.3803	-0.0052	0.0881	-18.268	19.2186	-5.2922
5	3.0469	-1.5912	-0.4954	4.2405	-0.0693	5.0637	0.1187	-0.4205	0.2171	-0.2827	0.0391	-0.12	-0.0561	0.0062	-0.1578	0.0517	-0.0202	-0.0105	0.3023	0.0022	0.0675	-7.4858	18.3267	-9.0531
6	3.0921	-0.067	2.6899	0.5844	0.9105	4.0204	0.3229	-0.0937	-0.4778	0.15	0.0289	0.0586	0.6838	0.0579	-0.3518	0.3993	0.0302	-0.0505	0.3077	-0.0044	0.1354	-4.3051	7.3319	-13.6555
7	0.645	0.4468	1.3312	4.9179	-0.6394	3.2887	0.0525	0.5123	-0.2276	-0.0691	0.2712	-0.6576	0.071	1.082	-0.3237	0.3556	0.045	0.0279	0.5779	-0.1125	0.3178	0.7349	11.0759	-24.5666
8	2.0525	-2.8752	5.2961	20.5253	-9.656	14.013	0.1409	0.019	0.2329	1.1491	-0.9512	-0.5123	0.1869	0.1817	0.8103	0.6695	0.1704	-0.0013	0.6893	-0.0565	0.7202	-3.5578	-2.0353	-18.1217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	78 - 82
2	X-RAY DIFFRACTION	2	A	83 - 96
3	X-RAY DIFFRACTION	3	A	97 - 113
4	X-RAY DIFFRACTION	4	A	114 - 130
5	X-RAY DIFFRACTION	5	A	131 - 172
6	X-RAY DIFFRACTION	6	A	173 - 193
7	X-RAY DIFFRACTION	7	A	194 - 204
8	X-RAY DIFFRACTION	8	A	205 - 214

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