PDB-5h75: Crystal structure of the MrsD-Protein A fusion protein

ID or keywords:

Entry

Database: PDB / ID: 5h75

Title

Crystal structure of the MrsD-Protein A fusion protein

Components

Mersacidin decarboxylase,Immunoglobulin G-binding protein A

Keywords

LYASE / synthetic protein

Function / homology

Function and homology information

Lyases; Carbon-carbon lyases; Carboxy-lyases / IgG binding / antibiotic biosynthetic process /

oxidoreductase activity /

lyase activity / extracellular region
Similarity search - Function

Biological species

Bacillus sp. (bacteria)

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.738 Å

Authors

Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.

Citation

Journal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.

History

Deposition	Nov 17, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 28, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5h75.cif.gz	355.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5h75.ent.gz	294.1 KB	Display	PDB format
PDBx/mmJSON format	5h75.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h7/5h75 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h75	HTTPS FTP

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Related structure data

Related structure data	5h76C 5h77C 5h78C 5h79C 5h7aC 5h7bC 5h7cC 5h7dC 5x3fC 5xbyC 1p3yS 2spzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2h3e-1 4kgx-1 9002 4kgv-1 1pvv-1 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	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

B: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

C: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

D: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

hetero molecules

108 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

B: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

C: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

D: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

hetero molecules

A: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

B: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

C: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

D: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

hetero molecules

A: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

B: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

C: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

D: Mersacidin decarboxylase,Immunoglobulin G-binding protein A

hetero molecules

defined by author&software
325 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	167.729, 167.729, 167.729
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	198
Space group name H-M	P2₁3

Components on special symmetry positions

ID	Model	Components
1	1	D-406- HOH

#1: Antibody	Mersacidin decarboxylase,Immunoglobulin G-binding protein A / Mersacidin-modifying enzyme MrsD / IgG-binding protein A / Staphylococcal protein A Mass: 26267.137 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-184,223-269 / Mutation: K182Q,G240A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (strain HIL-Y85/54728) (bacteria), (gene. exp.) Staphylococcus aureus (bacteria) Strain: HIL-Y85/54728 / Gene: mrsD, spa / Production host: Escherichia coli (E. coli) References: UniProt: Q9RC23, UniProt: P38507, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.07 Å³/Da / Density % sol: 69.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 5.5 / Details: 0.94M sodium citrate pH 5.5

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 39652 / % possible obs: 92 % / Redundancy: 3.3 % / Net I/σ(I): 22.1
Reflection shell	Resolution: 2.7→2.8 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1P3Y, 2SPZ

1p3y

2spz

Resolution: 2.738→30.623 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2434	1998	5.05 %
R_work	0.2039	-	-
obs	0.2059	39561	95.17 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.738→30.623 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6588	0	212	12	6812

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6951
X-RAY DIFFRACTION	f_angle_d	0.877	9464
X-RAY DIFFRACTION	f_dihedral_angle_d	14.093	4132
X-RAY DIFFRACTION	f_chiral_restr	0.051	1070
X-RAY DIFFRACTION	f_plane_restr	0.006	1172

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7379-2.8063	0.3214	130	0.2943	2520	X-RAY DIFFRACTION	91
2.8063-2.8822	0.3116	148	0.2748	2734	X-RAY DIFFRACTION	98
2.8822-2.9669	0.2898	146	0.2731	2727	X-RAY DIFFRACTION	98
2.9669-3.0626	0.3025	152	0.273	2748	X-RAY DIFFRACTION	98
3.0626-3.1719	0.2458	143	0.2404	2737	X-RAY DIFFRACTION	98
3.1719-3.2988	0.2895	145	0.2246	2761	X-RAY DIFFRACTION	98
3.2988-3.4487	0.2507	151	0.2164	2759	X-RAY DIFFRACTION	98
3.4487-3.6303	0.2548	143	0.2024	2737	X-RAY DIFFRACTION	98
3.6303-3.8573	0.2681	147	0.2035	2747	X-RAY DIFFRACTION	98
3.8573-4.1545	0.2304	144	0.1739	2757	X-RAY DIFFRACTION	97
4.1545-4.5713	0.1871	149	0.1635	2731	X-RAY DIFFRACTION	97
4.5713-5.23	0.183	141	0.1597	2699	X-RAY DIFFRACTION	95
5.23-6.5784	0.2663	140	0.2164	2715	X-RAY DIFFRACTION	95
6.5784-30.6249	0.2641	119	0.2236	2191	X-RAY DIFFRACTION	74

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	3.5418	-1.228	-0.4194	5.9483	-1.1918	5.9356	0.0314	0.0022	-1.3954	-0.799	-0.1908	0.1678	1.3	-0.7113	0.191	0.8476	-0.149	0.0915	0.6151	0.013	1.0382	-16.0283	-14.8597	11.4974
2	7.142	-2.997	0.9654	4.0394	0.0552	8.2458	0.1376	0.4114	0.7547	-0.9031	0.0235	-0.2399	-0.4217	0.4734	-0.1089	0.6966	-0.0826	0.1631	0.6772	0.1013	0.8582	-9.9394	-6.7856	9.4362
3	2.0968	-0.9805	-2.4912	5.7589	0.8515	8.2128	-0.2771	0.1617	-0.4157	0.0976	0.0797	1.1276	0.446	-0.9134	0.1708	0.4656	-0.1093	0.0156	0.8078	0.2119	1.0722	-23.4335	-3.36	21.2702
4	-0.1299	-0.0945	0.9699	3.8105	-3.3306	5.2458	-0.3799	-0.3402	-0.0865	0.4287	0.3911	0.3978	0.054	-0.2078	0.0227	0.876	-0.0875	0.2622	0.9281	0.1321	1.3222	-17.2079	-13.9941	30.0008
5	6.2979	-1.0488	-0.836	5.6086	2.9897	6.1809	0.0397	0.8691	-1.9139	0.2781	0.2682	1.7667	1.1796	-1.9205	-0.2044	1.0439	-0.4453	0.071	1.3039	0.1901	1.4776	-30.4008	-17.1926	14.3633
6	4.6729	4.1438	-1.4139	8.3307	0.5058	6.6212	-0.7425	1.1545	-0.339	-0.72	-0.537	2.1149	1.0527	-2.138	1.2633	1.4751	-0.3955	-0.2505	2.1023	-0.1555	2.5197	-44.2035	-16.2095	14.7583
7	6.3374	-2.0652	-6.8264	6.612	1.7539	7.3903	-0.904	2.3001	-0.7519	1.3731	-0.7082	1.4226	0.9456	-2.1278	1.4507	1.6461	-0.2907	-0.2061	1.6981	-0.2381	2.0114	-41.7112	-21.3783	7.3055
8	3.4843	1.1137	-0.4401	0.323	0.325	6.515	-0.0325	0.7549	0.7382	-0.2818	0.1527	0.5091	-1.0399	-0.5947	-0.0016	0.6419	0.2253	-0.0068	0.9046	0.2945	0.8504	-20.819	28.7157	5.4267
9	2.6198	0.2312	-3.1929	4.6243	4.8187	2.2718	-0.1244	-0.4485	-0.2461	0.2386	0.3592	-0.3883	-0.0649	0.3473	-0.1333	0.6874	0.1882	0.0065	0.8488	0.2794	0.8444	-11.7994	24.2696	8.6106
10	2.139	1.8761	1.2116	5.4321	-0.9354	6.1983	-0.0517	0.2167	0.2796	-0.0169	0.2733	0.9494	-0.2019	-1.2255	-0.2912	0.4853	0.1542	0.0164	1.0583	0.2496	0.901	-26.7674	16.6586	15.5583
11	1.5541	-1.5193	-1.0241	4.4624	-2.952	5.2187	-0.2588	-0.5421	-0.0056	0.0029	0.7618	0.9802	-0.3385	-1.5398	-0.5514	0.6849	0.2719	-0.099	1.6454	0.4384	1.2225	-33.4312	25.1434	9.091
12	5.215	-2.2918	-1.8692	8.8051	0.6851	2.0196	-1.1773	-1.6656	0.6783	1.0137	0.2892	0.6863	1.1777	-1.1353	0.7268	1.4314	0.6907	0.1951	2.3993	0.451	1.3005	-43.7956	36.2757	18.7891
13	8.1939	-5.002	-6.1461	8.0917	6.979	2.0134	0.1705	-0.8971	1.0035	-0.3748	0.514	-0.1036	-1.403	-1.3363	-0.9819	1.2298	0.5695	-0.0305	2.1601	0.3936	1.5929	-38.3909	43.3261	16.1496
14	4.8855	1.7123	0.9633	7.4091	0.662	6.6977	0.1023	-0.6175	-0.2968	0.7814	0.1932	0.1749	0.0421	-0.3675	-0.3525	0.4894	0.0929	0.0821	0.5909	0.1296	0.6033	-2.8902	13.6723	40.5864
15	9.4787	0.2426	1.7993	4.5413	-0.0738	5.7201	-0.0347	-0.1746	-0.2666	0.3532	0.3912	0.6597	-0.2318	-0.847	-0.3258	0.5562	0.0646	0.2197	0.6706	0.2545	0.6913	-15.562	10.7424	34.9526
16	3.8635	3.0435	0.5546	7.344	-1.1879	4.5162	0.2054	-0.3849	1.5943	0.737	0.471	2.0929	-1.1674	-0.8777	-0.6692	0.9139	0.2042	0.451	0.878	0.1693	1.175	-18.763	20.4168	42.0127
17	2.3444	7.5401	-2.3423	2.1723	-1.1182	7.8038	0.7167	-1.239	0.2101	1.5241	-0.6846	1.2039	0.1733	-1.0907	0.0489	0.991	0.1729	0.2243	1.1991	0.2221	1.1229	-16.4817	11.4315	51.3842
18	4.7476	2.0663	-2.5517	5.6005	-3.543	8.4398	-0.213	-1.0702	0.5721	1.9198	-0.3476	2.3664	0.9841	-0.5363	0.7513	1.471	-0.0169	0.4821	1.9879	0.6429	2.138	-27.7778	5.9176	57.31
19	9.7346	6.5369	-2.1171	7.592	-0.6763	4.7508	-0.4855	-2.6333	-1.1832	2.1929	-1.7737	0.9063	0.9454	-0.0737	2.1249	2.4858	-0.1563	0.6352	2.0871	-0.0416	1.3621	-20.2121	3.6129	62.4583
20	5.1151	-2.1643	-2.3081	4.3059	3.2576	4.5144	0.42	-0.5657	1.366	-0.1422	0.2213	0.2435	-0.9438	-0.4824	-0.5273	0.7052	0.0945	0.1602	0.5404	0	0.9984	4.938	45.0197	34.3295
21	6.8851	0.563	0.6754	2.5852	-0.6166	1.5581	0.03	0.0538	0.3277	0.1538	0.1853	0.2502	-0.379	-0.107	-0.2124	0.5248	0.0756	0.128	0.3887	-0.0228	0.4272	13.0743	34.6306	31.5933
22	2.4035	-0.6911	0.3572	9.3663	-1.6475	1.3016	-0.0283	-1.4027	-0.5199	0.6728	-0.0657	0.5018	0.2317	0.0921	0.0164	0.981	0.1211	0.1761	0.9633	0.0697	0.7608	14.4221	29.4855	45.256
23	2.4838	2.0576	0.0943	6.6444	-0.0815	1.3663	-0.1603	-0.3651	0.5859	0.0051	0.202	0.1207	-0.291	0.1431	0.017	0.8744	0.0994	0.2622	0.65	-0.1597	0.9561	13.1198	53.0235	41.4895

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 143 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 144 through 172 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 173 through 190 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 210 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 211 through 229 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 7 through 42 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 81 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 82 through 143 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 144 through 190 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 191 through 210 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 211 through 229 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 5 through 58 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 59 through 143 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 144 through 172 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 173 through 190 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 191 through 210 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 211 through 229 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid -3 through 18 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 19 through 143 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 144 through 163 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 164 through 229 )

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