PDB-5jd5: Crystal structure of MGS-MilE3, an alpha/beta hydrolase enzyme fr...

ID or keywords:

Entry

Database: PDB / ID: 5jd5

Title

Crystal structure of MGS-MilE3, an alpha/beta hydrolase enzyme from the metagenome of pyrene-phenanthrene enrichment culture with sediment sample of Milazzo Harbor, Italy

Components

MGS-MilE3

Keywords

HYDROLASE /

alpha/beta hydrolase /

esterase /

metagenome

Function / homology

Alpha/Beta hydrolase fold, catalytic domain /

Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Function and homology information

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Stogios, P.J. / Xu, X. / Cui, H. / Martinez-Martinez, M. / Chernikova, T.N. / Golyshin, P.N. / Yakimov, M.M. / Ferrer, M. / Savchenko, A.

Citation

Journal: To Be Published
Title: Crystal structure of MGS-MilE3, an alpha/beta hydrolase enzyme from the metagenome of pyrene-phenanthrene enrichment culture with sediment sample of Milazzo Harbor, Italy
Authors: Martinez-Martinez, M.

History

Deposition	Apr 15, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5jd5.cif.gz	528.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5jd5.ent.gz	439.2 KB	Display	PDB format
PDBx/mmJSON format	5jd5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/5jd5 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jd5	HTTPS FTP

-
Related structure data

Related structure data	2wir PDB Unreleased entryS 5jd3 5jd4 5jd6 S: Starting model for refinement
Similar structure data	4gdj-1 1j9y-d 3wdq-d 5eem-2 6vyc-1 6uob-2 2z2b-d 6q0z-1 5ef7-2 6wyq-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) Search similar-shape structures by Omokage search (details) 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

Related structure data

2wir
PDB Unreleased entryS

5jd3

5jd4

5jd6

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MGS-MilE3

B: MGS-MilE3

C: MGS-MilE3

D: MGS-MilE3

hetero molecules

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

1

A: MGS-MilE3

hetero molecules

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

2

B: MGS-MilE3

hetero molecules

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

3

C: MGS-MilE3

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

4

D: MGS-MilE3

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

5

A: MGS-MilE3

C: MGS-MilE3

hetero molecules

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

6

B: MGS-MilE3

D: MGS-MilE3

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.668, 97.160, 167.670
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	MGS-MilE3 Mass: 34810.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2009 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.12 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 30% (w/v) PEG4K, 1/70 chymotrypsin. Cryoprotectant: paratone-N oil.

-
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: Jul 16, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.95→24.72 Å / Num. obs: 103264 / % possible obs: 94.1 % / Redundancy: 2.7 % / R_merge(I) obs: 0.08 / Net I/σ(I): 15.63
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.574 / Mean I/σ(I) obs: 2.16 / % possible all: 97.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2WIR

2wir
PDB Unreleased entry

Resolution: 1.95→24.72 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.27

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.237	2006	1.95 %	Random
R_work	0.195	-	-	-
obs	0.196	103051	93.9 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.95→24.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9696	0	2	2015	11713

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9972
X-RAY DIFFRACTION	f_angle_d	0.993	13585
X-RAY DIFFRACTION	f_dihedral_angle_d	11.994	3590
X-RAY DIFFRACTION	f_chiral_restr	0.035	1457
X-RAY DIFFRACTION	f_plane_restr	0.005	1827

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 (%)
1.95-1.9972	0.2793	144	0.2958	7308	X-RAY DIFFRACTION	96
1.9972-2.0512	0.2878	146	0.2824	7462	X-RAY DIFFRACTION	98
2.0512-2.1115	0.3366	155	0.2688	7359	X-RAY DIFFRACTION	97
2.1115-2.1796	0.3092	137	0.2509	7352	X-RAY DIFFRACTION	96
2.1796-2.2575	0.3104	145	0.2605	7285	X-RAY DIFFRACTION	96
2.2575-2.3478	0.2773	136	0.2287	7174	X-RAY DIFFRACTION	94
2.3478-2.4545	0.2959	142	0.2159	7143	X-RAY DIFFRACTION	94
2.4545-2.5838	0.2667	140	0.2139	6950	X-RAY DIFFRACTION	91
2.5838-2.7455	0.2626	145	0.2032	6687	X-RAY DIFFRACTION	88
2.7455-2.9572	0.2613	137	0.197	6734	X-RAY DIFFRACTION	87
2.9572-3.2542	0.2232	130	0.1879	6940	X-RAY DIFFRACTION	90
3.2542-3.7237	0.1886	146	0.1614	7380	X-RAY DIFFRACTION	95
3.7237-4.6862	0.1895	149	0.1429	7632	X-RAY DIFFRACTION	98
4.6862-24.7174	0.1814	154	0.1494	7639	X-RAY DIFFRACTION	95

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	2.0947	-1.377	1.6214	3.4722	-1.367	2.1842	-0.0763	-0.2772	0.001	0.458	0.1203	0.0931	0.3276	-0.2562	-0.0645	0.4196	-0.0772	-0.1102	0.218	0.0175	0.2601	40.6389	47.7257	126.281
2	4.1172	3.6934	0.0412	5.8286	0.487	8.7778	-0.0478	-1.6879	0.4661	1.7197	-0.2773	0.2368	-0.8235	0.5913	0.3473	1.0868	-0.0232	0.011	0.6372	-0.0394	0.3843	31.3581	68.4708	134.6385
3	3.5216	-0.6341	1.8176	2.1417	0.3211	3.7999	-0.1103	-0.2326	0.0823	0.6211	0.1326	-0.1217	-0.1201	0.0683	0.0952	0.3781	-0.0002	-0.1175	0.178	-0.04	0.2021	46.6941	76.8379	126.6165
4	0.7471	-0.1074	0.0848	1.0979	0.3632	1.1913	-0.032	-0.0782	0.0485	0.2277	-0.0091	-0.0295	-0.0874	-0.0664	0.0489	0.2521	0.0075	-0.1126	0.191	-0.0137	0.1935	42.1885	68.5072	116.3991
5	0.781	0.2269	0.6574	2.1358	-0.1729	2.8878	-0.0494	-0.0439	-0.0635	0.228	0.0112	-0.1535	0.0117	-0.0422	0.0029	0.1874	0.003	-0.1132	0.1442	-0.0036	0.2045	46.4246	58.4572	112.1875
6	1.6906	2.1215	-1.1291	5.2556	-1.1284	1.2438	-0.0828	0.3657	0.1796	-0.4123	0.1691	0.3464	-0.161	-0.0534	-0.0871	0.2996	0.1035	-0.0752	0.2897	0.0198	0.2218	39.8544	78.0657	41.3118
7	7.2026	6.0285	-3.4233	7.2274	-4.0164	2.2334	-0.1989	1.0705	-0.238	-1.2926	0.1505	-0.3433	-0.0365	-0.4691	0.0376	0.8744	0.1729	-0.1706	0.6637	-0.1165	0.3333	35.0493	61.104	31.618
8	0.2567	0.0679	-0.0497	1.445	0.3791	1.3296	0.0036	0.0579	-0.0554	-0.0229	-0.0171	-0.0209	0.0956	0.0242	0.0188	0.1847	0.0086	-0.0719	0.1714	-0.0017	0.1851	43.1654	57.4191	49.9655
9	1.9812	0.401	-0.9103	2.7183	-0.7866	3.8747	-0.0039	0.0068	-0.0397	-0.1452	0.0408	-0.004	0.0869	0.0126	-0.0308	0.2251	0.0027	-0.0881	0.1081	-0.0269	0.1638	42.5667	69.24	57.5841
10	5.2171	-2.8281	2.322	4.274	-5.3878	7.4284	-0.1175	-0.0049	0.0488	0.0013	0.0026	-0.5758	-0.1377	0.5142	0.0949	0.2267	-0.0007	-0.0349	0.2999	-0.0396	0.2754	57.7577	67.8942	49.0669
11	2.8929	0.3525	-1.6252	3.7759	-0.5174	2.8291	0.0089	0.0525	0.2782	0.0416	-0.0953	-0.2232	-0.2282	0.6101	0.1718	0.259	-0.0269	-0.0688	0.1368	0.0011	0.2138	48.138	52.9868	83.5405
12	3.1643	-1.5348	-0.5227	6.4385	0.1968	4.5486	-0.1996	0.8923	-0.1033	-1.4589	-0.0554	0.229	-0.0105	-0.5693	0.247	0.6252	-0.0986	-0.1968	0.6188	-0.0478	0.339	26.4229	44.4915	74.0957
13	0.8221	-0.3157	-0.133	1.4658	0.4236	1.7991	-0.0213	0.0901	-0.1107	-0.0754	-0.0494	0.2216	0.4733	-0.2735	0.0532	0.3415	-0.0974	-0.1075	0.2539	-0.0237	0.2903	31.7795	29.2322	90.6549
14	0.3086	0.0753	-0.2339	2.1804	-0.1599	2.6856	-0.0721	0.0169	0.054	0.1031	-0.0087	0.2234	0.0216	-0.2613	0.047	0.1522	-0.0358	-0.1151	0.2199	-0.0135	0.2426	34.1978	47.2826	96.6367
15	2.0208	0.0517	-1.3589	4.0238	0.6942	1.1652	-0.0677	0.115	0.009	-0.0483	0.0592	-0.3963	0.3959	0.1568	-0.0417	0.2405	-0.0409	-0.1132	0.1863	-0.0229	0.2372	48.2752	38.2362	91.36
16	6.3018	-0.5901	-1.2774	1.825	1.0822	6.2562	-0.0375	0.0849	-0.3702	-0.1423	0.0491	-0.0484	0.235	0.4527	-0.0736	0.3183	0.0221	-0.1701	0.1407	-0.0204	0.2683	47.8758	74.8255	83.615
17	4.0163	2.0751	3.4706	8.2036	2.2888	5.835	-0.2623	-0.5302	-0.0999	1.4559	0.3681	-0.6348	-0.67	0.3985	-0.107	0.4612	0.0445	-0.1266	0.4778	-0.0073	0.3401	26.2766	83.4493	93.6916
18	1.4631	1.3366	-0.3524	2.4144	0.5224	1.3964	0.0372	-0.0201	0.2172	0.038	-0.0754	0.107	-0.3179	-0.0621	0.0132	0.314	0.0533	-0.091	0.1557	-0.0232	0.2385	32.1419	98.4254	78.7236
19	0.6139	0.289	-0.0109	2.0615	-0.268	2.2896	0.0482	0.0173	0.0089	-0.0603	-0.0528	0.1314	-0.172	-0.1476	-0.0112	0.2073	0.0174	-0.0948	0.1717	-0.0193	0.1969	33.6116	82.4015	69.9333
20	3.7546	-0.0971	0.9424	2.5515	2.1272	2.0606	0.001	-0.1671	0.1566	0.2885	-0.0723	-0.3762	-0.3992	0.2995	0.0647	0.3075	-0.0622	-0.0941	0.2239	-0.0273	0.2333	48.3763	89.9068	76.0409

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 5:40)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 41:54)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 55:86)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 87:234)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 235:321)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 4:44)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 45:59)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 60:233)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 234:301)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 302:321)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 6:36)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 37:54)
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 55:191)
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESID 192:283)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 284:320)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 5:37)
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 38:54)
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 55:179)
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 180:283)
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 284:321)

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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