PDB-4q3l: Crystal structure of MGS-M2, an alpha/beta hydrolase enzyme from ...

ID or keywords:

Entry

Database: PDB / ID: 4q3l

Title

Crystal structure of MGS-M2, an alpha/beta hydrolase enzyme from a Medee basin deep-sea metagenome library

Components

MGS-M2

Keywords

HYDROLASE / metagenome / metagenomic library / alpha and beta proteins / alpha/beta hydrolase superfamily / esterase/lipase fold

Function / homology

Function and homology information

TAP-like protein / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.01 Å

Authors

Stogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A.

Citation

Journal: Environ Microbiol / Year: 2015
Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.
Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...

History

Deposition	Apr 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	Sep 20, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4q3l.cif.gz	895.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4q3l.ent.gz	751.6 KB	Display	PDB format
PDBx/mmJSON format	4q3l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4q3l_validation.pdf.gz	462.4 KB	Display	wwPDB validaton report
Full document	4q3l_full_validation.pdf.gz	483.6 KB	Display
Data in XML	4q3l_validation.xml.gz	43.5 KB	Display
Data in CIF	4q3l_validation.cif.gz	64.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3l ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3l	HTTPS FTP

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Related structure data

Related structure data	4q3kC 4q3mC 4q3nC 4q3oC 1cr6S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4mz7-d 4rxp-d 5y1b-2 5wp5-d 5swc-d 3vtr-2 3r4i-2 3tml-2 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: MGS-M2

B: MGS-M2

C: MGS-M2

D: MGS-M2

E: MGS-M2

F: MGS-M2

G: MGS-M2

H: MGS-M2

hetero molecules

273 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MGS-M2

B: MGS-M2

C: MGS-M2

D: MGS-M2

hetero molecules

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

2

E: MGS-M2

F: MGS-M2

G: MGS-M2

H: MGS-M2

hetero molecules

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

Unit cell

Length a, b, c (Å)	105.568, 139.134, 111.109
Angle α, β, γ (deg.)	90.00, 89.94, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	MGS-M2 Mass: 34064.723 Da / Num. of mol.: 8 / Fragment: MGS-M2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Gene: MGS-M2 / Plasmid: p15-TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KBT7*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H₂O
Source details	THE SAMPLE WAS EXTRACTED FROM MEDEE BASIN DEEP-SEA AND ANALYZED BY USING METAGENOME LIBRARY TECHNIQUE

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.92 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: protein treated with thermolysin in 1/10 molar ratio crystallization in: 0.1 M sodium Hepes, 1.4 M sodium citrate, cryoprotectant: 15% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 28, 2014
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3→32 Å / Num. obs: 63183 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.6 % / R_merge(I) obs: 0.093 / Net I/σ(I): 17.08
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.536 / Mean I/σ(I) obs: 3.66 / % possible all: 100

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Processing

Software

Name	Version	Classification
StructureStudio		data collection
PHENIX	(phenix.phaser)	model building
PHENIX	(phenix.refine: dev_1631)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1CR6

1cr6

Resolution: 3.01→31.669 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 28.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2554	1992	3.16 %
R_work	0.2012	-	-
obs	0.2029	63067	99.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.01→31.669 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17910	0	12	292	18214

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	18357
X-RAY DIFFRACTION	f_angle_d	0.711	24935
X-RAY DIFFRACTION	f_dihedral_angle_d	12.686	6717
X-RAY DIFFRACTION	f_chiral_restr	0.029	2817
X-RAY DIFFRACTION	f_plane_restr	0.003	3138

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 (%)
3.0103-3.0855	0.3639	133	0.2736	3994	X-RAY DIFFRACTION	92
3.0855-3.1689	0.3465	145	0.2709	4368	X-RAY DIFFRACTION	100
3.1689-3.262	0.3443	154	0.2419	4338	X-RAY DIFFRACTION	100
3.262-3.3672	0.3096	131	0.2363	4431	X-RAY DIFFRACTION	100
3.3672-3.4874	0.3174	141	0.2332	4367	X-RAY DIFFRACTION	100
3.4874-3.6268	0.2935	136	0.2121	4358	X-RAY DIFFRACTION	100
3.6268-3.7916	0.268	144	0.1954	4388	X-RAY DIFFRACTION	100
3.7916-3.9912	0.2678	148	0.1878	4359	X-RAY DIFFRACTION	100
3.9912-4.2407	0.2315	146	0.178	4406	X-RAY DIFFRACTION	100
4.2407-4.5672	0.2279	138	0.1685	4350	X-RAY DIFFRACTION	100
4.5672-5.0252	0.1952	139	0.1638	4444	X-RAY DIFFRACTION	100
5.0252-5.7486	0.2233	146	0.1842	4383	X-RAY DIFFRACTION	100
5.7486-7.2284	0.2436	144	0.2161	4427	X-RAY DIFFRACTION	100
7.2284-31.6708	0.1992	147	0.1922	4462	X-RAY DIFFRACTION	99

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	4.5065	-4.6529	-3.1555	8.2249	1.9092	2.744	1.592	0.1762	0.34	-0.6852	-1.0445	0.5633	0.2157	-1.9097	-0.5743	0.693	0.0393	-0.1185	0.8956	0.022	0.3949	103.458	-8.3299	34.8223
2	8.3607	-1.3484	0.8967	4.5954	3.0446	5.225	0.1591	0.2686	0.7652	-0.139	0.0673	0.1579	-0.64	0.209	-0.2411	0.4822	0.0236	-0.0056	0.2762	0.0327	0.4492	119.7014	-12.5434	33.5314
3	1.0246	-0.2874	-0.3348	2.8499	-0.4659	2.6813	-0.0109	0.1676	0.1156	-0.187	-0.0145	0.0124	-0.1408	-0.2573	0.0327	0.3062	-0.0132	-0.0248	0.3085	-0.0015	0.3633	113.3072	-26.7576	34.123
4	6.3917	0.0972	-0.3071	4.9154	1.2307	2.8034	0.1429	0.6243	0.0975	-0.7056	-0.2562	-0.169	0.4168	-0.2145	0.0996	0.4219	0.0235	0.0544	0.3159	0.0094	0.3585	127.1117	-26.3988	22.9324
5	1.9948	-0.4712	-3.4493	7.2676	1.9585	8.4653	0.0112	-1.127	-0.5659	1.6252	0.2714	-0.3029	0.8363	0.7263	-0.1724	0.4933	-0.0363	-0.0562	0.7058	0.1939	0.5451	116.7561	-70.7595	61.3303
6	2.2985	1.8157	-0.3478	3.5963	-0.5788	7.0857	-0.2864	-0.245	-0.6627	-0.1061	-0.0053	-0.0127	0.5754	0.183	0.2463	0.4287	0.0078	-0.0016	0.3659	0.0624	0.6387	117.2169	-71.2337	44.1727
7	1.5206	-0.27	-0.5077	2.7529	0.2423	1.3637	0.046	-0.1625	-0.1425	0.0287	-0.0006	-0.0135	0.0664	0.0745	-0.0408	0.2804	-0.0325	-0.0254	0.3348	0.0528	0.3307	119.9535	-56.4465	46.3834
8	3.4663	-0.4195	-1.0037	4.8965	-0.2977	3.8932	-0.0212	-0.2958	-0.1015	-0.2842	-0.0881	-0.5827	0.2403	0.2768	0.1155	0.3909	-0.0052	0.0405	0.3218	0.0457	0.4237	129.1952	-62.21	32.5221
9	8.9977	1.2102	-0.5932	2.4179	1.0776	7.6119	0.2093	0.0194	0.5263	0.1106	0.2113	-0.0582	-0.6089	0.6526	-0.3859	0.4999	-0.077	0.0054	0.4375	0.1227	0.4835	153.8998	-17.775	12.6429
10	5.2541	0.5316	-0.7511	4.5429	0.196	3.3774	0.0097	-0.0878	0.4218	0.3164	0.0687	0.0456	-0.1487	0.2412	-0.0533	0.4133	-0.0911	0.0015	0.3672	0.0457	0.3662	152.3323	-23.432	18.3008
11	5.6968	0.537	-0.7182	1.7147	-0.789	1.9692	-0.1371	0.3413	0.4929	-0.0239	-0.0871	0.1375	0.0715	0.1494	0.2051	0.4069	0.0026	-0.0644	0.34	-0.0275	0.3304	147.0923	-40.5905	6.123
12	2.5034	-0.8414	0.9362	3.8324	0.6656	1.5276	0.0092	-0.2012	0.1775	0.2061	-0.0846	0.2151	-0.0322	0.1628	0.0911	0.4663	-0.0678	0.0776	0.3837	0.0768	0.3336	140.7366	-31.6583	26.1873
13	5.3677	-3.2191	-1.1103	5.4184	3.2601	2.1891	0.129	0.4197	-0.6418	0.1877	-0.376	0.4709	0.7913	-0.4212	0.1945	0.5825	-0.0586	0.0447	0.4588	-0.0467	0.5048	132.6357	-79.7264	8.0195
14	5.0598	-0.1238	-3.4139	2.657	-0.3897	6.3226	-0.418	0.1627	-0.261	-0.2465	0.2405	0.162	0.8853	-0.4947	0.2513	0.4913	-0.0177	-0.0017	0.3121	-0.0281	0.4828	137.7943	-73.1135	11.0829
15	1.8465	0.6885	-0.5244	2.4992	0.2238	2.0362	-0.0462	0.2687	-0.0181	-0.0605	-0.0038	0.1116	0.2279	-0.1149	0.0511	0.3468	0.0247	-0.006	0.3478	0.0153	0.3612	135.8466	-61.8169	8.186
16	1.5364	1.4308	-1.5152	4.6953	-0.9957	4.8944	0.1343	0.0454	0.4172	-0.0185	-0.0966	0.6398	-0.0233	-0.4561	-0.0679	0.3477	0.0385	0.0211	0.3372	-0.0058	0.5078	126.8855	-59.5958	21.2425
17	7.79	0.9697	3.8314	6.8572	2.812	8.7029	0.2303	-0.6178	0.7415	-0.5031	-0.223	0.1784	-0.3039	-0.7091	-0.0796	0.5823	-0.0004	0.0595	0.3976	-0.0092	0.5636	185.7389	-42.3133	48.9905
18	2.7559	-0.4714	-0.3689	4.0826	-0.4208	6.513	-0.3769	-0.1589	0.1994	0.1185	0.0522	0.2578	-0.6223	-0.2165	0.356	0.3606	-0.031	-0.0334	0.3535	-0.0575	0.4581	184.3345	-52.0829	47.1281
19	1.3925	-0.1139	0.4903	2.0728	0.1158	1.2319	0.1105	-0.1826	0.0235	0.0496	-0.1366	0.0844	-0.0793	-0.0199	0.0227	0.3602	-0.0314	0.013	0.3626	0.0469	0.3698	193.514	-66.2759	46.7345
20	1.694	-1.7551	0.3424	4.2537	-1.3353	4.5194	0.0419	0.0002	-0.2741	0.3045	-0.1571	0.5934	0.0416	-0.237	0.1096	0.3472	-0.0406	-0.0214	0.3282	-0.0889	0.5602	179.6731	-64.3943	34.43
21	2.3015	0.5819	0.0288	9.6746	1.8016	2.2323	-0.2207	-0.8246	-0.7323	0.2379	-0.1653	0.1604	1.2765	-0.8277	0.2653	0.6846	-0.0762	0.0198	0.5906	0.0232	0.4934	165.2107	-117.041	23.2276
22	2.2843	0.294	-0.2778	4.3981	-0.0144	2.0631	-0.0371	-0.139	-0.3681	0.3448	0.1075	0.2388	0.2157	-0.2059	-0.0625	0.4464	-0.0242	-0.0144	0.3831	0.0289	0.3578	166.003	-104.3756	25.3434
23	2.6117	1.4844	1.2516	2.9445	0.0372	1.6746	0.2846	-0.0952	-0.3566	0.0114	-0.1795	-0.2586	0.2378	-0.0789	-0.1372	0.3586	0.0558	0.0235	0.3979	0.04	0.3269	171.461	-89.7727	8.9717
24	1.8954	-0.6004	0.4665	1.9471	0.2015	1.6434	0.0037	-0.3803	0.0152	0.493	0.0516	0.0016	-0.0258	-0.1659	-0.0434	0.4937	-0.0456	0.0226	0.3444	0.0324	0.4568	171.796	-95.2257	26.8053
25	3.9219	2.5811	1.0245	3.7691	0.2876	7.0805	0.3939	0.1852	-0.5541	-0.5873	-0.0238	-0.02	0.4691	0.6815	-0.3427	0.664	0.3069	-0.0975	0.6434	-0.0117	0.8132	209.3064	-109.9124	42.753
26	4.6383	-0.2982	-0.2078	4.2829	-0.2598	2.8607	0.0211	0.0537	-0.5011	-0.0709	0.0152	-0.057	0.2667	0.3324	-0.0533	0.4264	0.1037	-0.0235	0.39	0.0121	0.4138	205.1616	-100.4588	38.5645
27	1.6654	-0.0062	0.5462	1.7961	-0.3773	1.9633	-0.0987	-0.1297	-0.1332	0.0527	-0.0664	-0.0061	0.0102	0.1184	0.179	0.3272	-0.0188	0.0212	0.3052	0.0281	0.3795	200.6122	-85.0783	45.0677
28	2.3185	0.4874	-0.9549	5.3724	2.2637	1.9991	-0.045	0.126	-0.1334	-0.3522	-0.1325	0.3262	0.2291	0.1494	0.2016	0.4672	0.0708	-0.1329	0.3358	0.0872	0.425	191.0432	-93.1312	30.0636
29	3.1605	0.1821	0.4643	2.3836	-0.1803	2.9968	-0.0529	0.2339	0.3794	-0.0697	0.1498	-0.0579	-0.4236	0.0504	-0.0805	0.391	0.0646	-0.0078	0.3745	0.061	0.5993	169.2201	-53.5513	6.3965
30	1.045	-0.0995	0.7424	3.043	-0.7386	1.3397	0.0789	0.2611	0.0709	-0.0743	-0.1717	-0.1815	-0.0075	0.1564	0.1176	0.3087	0.0495	0.0383	0.3311	-0.0225	0.3559	174.0105	-67.6539	8.484
31	4.1206	0.8359	1.9869	4.7592	-0.9453	2.8197	-0.1596	0.1944	-0.2379	-0.0829	-0.0281	0.109	0.0751	-0.2314	0.1576	0.3674	0.0898	0.075	0.2856	0.02	0.3656	164.6326	-71.8256	7.4353
32	2.6846	-1.2902	-0.8832	3.3724	0.7063	4.3027	0.069	0.1535	0.3426	0.243	-0.1073	-0.5876	-0.2609	0.2643	0.0273	0.3403	0.0119	-0.0954	0.3075	0.0481	0.4778	182.6228	-65.2378	20.6372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:8 )	A	2 - 8
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 9:48 )	A	9 - 48
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 49:232 )	A	49 - 232
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 233:276 )	A	233 - 276
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 2:9 )	B	2 - 9
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 10:45 )	B	10 - 45
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 46:232 )	B	46 - 232
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 233:276 )	B	233 - 276
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID -1:37 )	C	-1 - 37
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 38:121 )	C	38 - 121
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 122:197 )	C	122 - 197
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 198:276 )	C	198 - 276
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 2:31 )	D	2 - 31
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 32:68 )	D	32 - 68
15	X-RAY DIFFRACTION	15	( CHAIN D AND RESID 69:217 )	D	69 - 217
16	X-RAY DIFFRACTION	16	( CHAIN D AND RESID 218:276 )	D	218 - 276
17	X-RAY DIFFRACTION	17	( CHAIN E AND RESID 2:24 )	E	2 - 24
18	X-RAY DIFFRACTION	18	( CHAIN E AND RESID 25:115 )	E	25 - 115
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 116:213 )	E	116 - 213
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 214:276 )	E	214 - 276
21	X-RAY DIFFRACTION	21	( CHAIN F AND RESID 2:25 )	F	2 - 25
22	X-RAY DIFFRACTION	22	( CHAIN F AND RESID 26:134 )	F	26 - 134
23	X-RAY DIFFRACTION	23	( CHAIN F AND RESID 135:173 )	F	135 - 173
24	X-RAY DIFFRACTION	24	( CHAIN F AND RESID 174:276 )	F	174 - 276
25	X-RAY DIFFRACTION	25	( CHAIN G AND RESID -1:24 )	G	-1 - 24
26	X-RAY DIFFRACTION	26	( CHAIN G AND RESID 25:114 )	G	25 - 114
27	X-RAY DIFFRACTION	27	( CHAIN G AND RESID 115:209 )	G	115 - 209
28	X-RAY DIFFRACTION	28	( CHAIN G AND RESID 210:276 )	G	210 - 276
29	X-RAY DIFFRACTION	29	( CHAIN H AND RESID -3:68 )	H	-3 - 68
30	X-RAY DIFFRACTION	30	( CHAIN H AND RESID 69:166 )	H	69 - 166
31	X-RAY DIFFRACTION	31	( CHAIN H AND RESID 167:205 )	H	167 - 205
32	X-RAY DIFFRACTION	32	( CHAIN H AND RESID 206:276 )	H	206 - 276

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