PDB-4yam: Crystal structure of LigE-apo form from Sphingobium sp. strain SYK-6

ID or keywords:

Entry

Database: PDB / ID: 4yam

Title

Crystal structure of LigE-apo form from Sphingobium sp. strain SYK-6

Components

Beta-etherase

Keywords

TRANSFERASE / Glutathione-S-transferase B-etherase

Function / homology

Function and homology information

lignin catabolic process / hydrolase activity / plasma membrane
Similarity search - Function

Biological species

Sphingobium sp. SYK-6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.905 Å

Authors

Pereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.
Authors: Helmich, K.E. / Pereira, J.H. / Gall, D.L. / Heins, R.A. / McAndrew, R.P. / Bingman, C. / Deng, K. / Holland, K.C. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Donohue, T.J. / ...

History

Deposition	Feb 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references / Source and taxonomy
Revision 1.2	Jul 20, 2016	Group: Data collection

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yam.cif.gz	609.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4yam.ent.gz	533.1 KB	Display	PDB format
PDBx/mmJSON format	4yam.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4yam_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	4yam_full_validation.pdf.gz	458.6 KB	Display
Data in XML	4yam_validation.xml.gz	48.7 KB	Display
Data in CIF	4yam_validation.cif.gz	72.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ya/4yam ftp://data.pdbj.org/pub/pdb/validation_reports/ya/4yam	HTTPS FTP

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Related structure data

Related structure data	4xt0C 4yanC 4y98 4y9d 4ya6 4yac 4yae 4yag 4yai 4yap 4yav C: citing same article (ref.)
Similar structure data	4yan-1 4yan-2 3adu-2 4m1h-2 6nac-d 1goz-d 6jey-1 4wsh-d 4d8g-2 6e5a-1 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	#212 - Aug 2017 Glutathione Transferases similarity (4) #255 - Mar 2021 Cisplatin and DNA similarity (3)

Deposited unit

A: Beta-etherase

B: Beta-etherase

C: Beta-etherase

D: Beta-etherase

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

1

A: Beta-etherase

B: Beta-etherase

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

2

C: Beta-etherase

D: Beta-etherase

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

Unit cell

Length a, b, c (Å)	122.556, 97.155, 131.387
Angle α, β, γ (deg.)	90.00, 106.65, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Beta-etherase / Beta-aryl ether cleaving enzyme Mass: 32293.861 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligE / Production host: Escherichia coli (E. coli) / References: UniProt: P27457, UniProt: G2IN93*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1159 / 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: 2.92 Å³/Da / Density % sol: 57.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Ammonium Citrate, 0.1 M MES pH 5.5, 20 % PEG 3,350, 5% Isopropanol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99996 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99996 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 114153 / % possible obs: 99.2 % / Redundancy: 5 % / Net I/σ(I): 9

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.3_1479)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 1.905→50 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2713	1999	1.75 %
R_work	0.2272	-	-
obs	0.228	114138	99.16 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.905→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8246	0	0	1159	9405

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8512
X-RAY DIFFRACTION	f_angle_d	0.956	11611
X-RAY DIFFRACTION	f_dihedral_angle_d	13.552	3131
X-RAY DIFFRACTION	f_chiral_restr	0.035	1189
X-RAY DIFFRACTION	f_plane_restr	0.004	1520

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 (%)
1.9052-1.9529	0.3507	141	0.2894	7926	X-RAY DIFFRACTION	99
1.9529-2.0057	0.3361	144	0.2684	8052	X-RAY DIFFRACTION	100
2.0057-2.0647	0.2601	143	0.2501	8023	X-RAY DIFFRACTION	100
2.0647-2.1314	0.2833	143	0.2377	8004	X-RAY DIFFRACTION	100
2.1314-2.2075	0.2856	144	0.2344	8062	X-RAY DIFFRACTION	100
2.2075-2.2959	0.2911	144	0.2308	8062	X-RAY DIFFRACTION	100
2.2959-2.4004	0.28	143	0.2293	8033	X-RAY DIFFRACTION	100
2.4004-2.527	0.2921	143	0.2268	8041	X-RAY DIFFRACTION	100
2.527-2.6853	0.2695	143	0.2243	8023	X-RAY DIFFRACTION	99
2.6853-2.8926	0.3187	143	0.2337	8010	X-RAY DIFFRACTION	99
2.8926-3.1836	0.2787	143	0.2276	7990	X-RAY DIFFRACTION	99
3.1836-3.6442	0.2622	142	0.2153	7993	X-RAY DIFFRACTION	99
3.6442-4.5907	0.2365	142	0.2016	7968	X-RAY DIFFRACTION	98
4.5907-48.5933	0.2413	141	0.2308	7952	X-RAY DIFFRACTION	96

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	2.1616	0.7261	-0.8078	1.2689	0.6811	2.3061	0.057	0.0442	-0.0539	0.0342	0.0663	-0.2385	0.0569	0.2804	-0.081	0.1251	-0.0103	-0.0047	0.1708	0.0085	0.235	-15.3717	-14.2094	35.7368
2	0.4419	0.281	0.2975	-0.0581	-0.9421	3.4288	0.006	-0.0993	0.0541	0.0607	-0.0869	0.0066	-0.0113	0.1323	0.0918	0.1715	-0.0164	-0.0038	0.1756	-0.0055	0.1522	-30.6068	-3.5115	40.1308
3	5.1657	-0.6793	1.6948	1.2122	0.2859	1.0385	-0.3933	-0.5331	0.4997	0.0986	0.1989	-0.1912	-0.1718	-0.162	0.1639	0.2472	-0.043	-0.0412	0.2972	-0.0623	0.2079	-26.6738	0.1648	54.9511
4	1.8372	-0.4493	-0.4969	1.2028	0.0681	2.1503	0.1241	0.005	0.0227	0.0182	-0.0889	-0.0429	0.1009	-0.1154	-0.0006	0.1147	-0.0266	-0.0067	0.1001	0.0241	0.1297	-36.0045	-12.048	34.5439
5	2.8956	-0.8489	0.1346	3.1481	0.5042	1.8119	0.0187	-0.2186	-0.2262	0.1332	-0.0773	0.1983	0.0136	-0.1671	0.0503	0.1411	-0.0769	0.0167	0.1821	0.0336	0.1524	-39.8537	-14.8391	44.8749
6	1.9191	0.486	0.0265	0.9454	-0.2617	1.3871	0.0736	0.2017	-0.0497	-0.2004	-0.0542	0.155	-0.1388	-0.3786	-0.0068	0.2277	0.0094	-0.0919	0.3195	-0.0222	0.1601	-49.6473	0.7904	4.7703
7	5.3914	-0.6694	1.1832	1.5788	0.2287	1.5226	0.0901	0.0588	-0.1996	-0.2575	-0.1483	0.0506	0.2043	-0.367	0.0082	0.2168	-0.0249	-0.0549	0.2735	-0.0579	0.1775	-45.9483	-10.2849	6.897
8	3.3331	-2.7654	-1.2118	7.5266	2.9552	2.9639	0.0447	0.1771	-0.2577	-0.4402	-0.1666	0.4107	-0.1023	0.2607	0.1237	0.1195	-0.0062	-0.0028	0.1971	0.0173	0.1547	-40.1479	-3.3691	23.9132
9	1.7812	0.1102	1.6833	0.0529	0.1481	2.0675	0.1666	-0.3379	-0.0602	-0.1483	-0.2888	0.4187	-0.1291	-1.0762	0.0896	0.2258	0.1266	-0.143	0.5275	-0.1113	0.4833	-59.6693	12.2279	20.0695
10	1.5256	-1.6914	-0.5524	3.2853	1.8254	2.7618	0.0771	0.1705	0.1847	-0.2192	-0.0874	-0.1114	-0.2113	-0.0397	-0.013	0.1285	-0.0293	0.0021	0.1174	0.0467	0.1255	-37.6052	7.9811	20.6598
11	1.712	0.2453	0.0885	1.9245	1.044	2.0388	-0.032	0.1085	0.2036	-0.2916	0.0296	-0.0102	-0.4841	-0.0579	0.019	0.2469	-0.0188	-0.032	0.1597	0.0637	0.1619	-36.8468	16.316	18.1653
12	2.5268	0.1037	-0.4784	1.3158	-0.017	0.655	0.1278	0.3465	0.2055	-0.4321	-0.0513	-0.3797	-0.1132	0.1991	-0.0224	0.3866	-0.0369	0.1357	0.2761	-0.0007	0.2678	-40.4352	-41.3524	4.4055
13	5.3664	-0.1551	-1.748	1.7845	-0.3821	3.0189	-0.126	0.0854	0.1866	-0.5239	0.0691	-0.3043	-0.321	0.193	-0.0305	0.4204	-0.0332	0.1359	0.2299	0.0562	0.2973	-43.9663	-30.2755	6.5456
14	1.1016	0.0709	-0.3177	0.4025	0.3342	1.342	-0.0152	-0.0029	0.0079	-0.2081	-0.0406	-0.4745	0.0016	0.1932	0.0117	0.1674	-0.0179	0.0949	0.1875	-0.0092	0.2545	-42.7906	-45.4695	21.397
15	2.5863	0.0447	1.2379	3.0768	-0.9954	5.8146	-0.0934	-0.7578	-0.0952	-0.1053	-0.6856	-0.2965	-1.6177	0.8297	-0.0011	0.2762	-0.1061	0.1649	0.6962	-0.0576	0.5376	-25.5865	-49.9935	18.9356
16	1.1816	-0.6333	0.2673	2.2517	-0.8741	2.798	-0.0228	0.0315	-0.118	-0.1196	-0.1064	-0.1073	0.1798	0.1375	0.1025	0.1629	-0.0359	0.0465	0.1314	-0.0187	0.1837	-49.755	-49.678	20.9876
17	0.2762	-0.4078	-0.6019	2.3956	-0.2209	1.8947	-0.0475	0.0514	-0.1377	-0.3444	0.0308	-0.103	0.3744	-0.0013	0.0239	0.2118	-0.0351	0.05	0.1837	-0.0325	0.24	-53.1294	-56.7458	18.0578
18	2.2527	0.8457	-0.1789	1.3589	-1.2758	1.8543	0.1413	-0.3725	0.2955	0.2628	-0.0876	0.2689	-0.2059	-0.135	-0.0838	0.1807	-0.0308	0.0615	0.2112	-0.0704	0.2577	-73.0462	-24.9302	40.9374
19	4.0884	0.3298	-1.7814	1.9716	-0.2035	3.424	0.0354	0.3467	-0.2831	-0.1091	-0.0795	0.3717	0.119	-0.3425	0.0555	0.1178	-0.0218	-0.0251	0.2056	-0.0677	0.3575	-75.6917	-28.0752	29.8083
20	1.4292	-0.1854	-0.7826	0.731	0.7489	2.7764	-0.0015	-0.1587	-0.2003	0.1284	-0.1539	0.0089	0.0893	-0.1329	0.1577	0.1759	-0.0566	0.03	0.1516	0.0112	0.2087	-59.7287	-36.6448	40.6874
21	5.7138	-4.6856	-0.6983	7.4439	0.3064	2.9241	0.4823	-0.936	-0.25	-0.0105	-0.2427	0.4056	-0.0045	0.1082	-0.0318	0.2835	-0.1297	0.0627	0.4125	0.083	0.3449	-71.5222	-40.2488	54.8268
22	1.9519	-2.3273	-0.4807	3.9199	0.0893	1.4	-1.111	-0.354	-0.3808	1.0707	0.4648	0.5045	0.4226	-0.0083	0.2844	0.3804	-0.1606	0.1146	0.4874	0.1934	0.2715	-60.7437	-44.6664	56.4678
23	3.229	0.1936	-0.7732	3.172	-1.2696	4.4324	0.1253	-0.3689	-0.3403	0.1243	-0.1254	-0.1917	0.4646	0.1968	-0.1038	0.1043	-0.0637	-0.0241	0.1856	0.032	0.1794	-47.0147	-35.6415	42.3594
24	5.3925	-2.2583	1.1398	4.8702	1.6054	3.4347	-0.178	0.4286	0.2634	-0.2553	-0.1333	-0.2837	-0.445	0.3611	0.2844	0.1688	-0.0403	0.0247	0.1471	0.0286	0.1873	-53.0423	-22.5485	27.2285
25	1.1734	-0.3047	0.5062	0.7219	0.469	3.1524	0.1271	-0.1297	-0.0286	0.0355	-0.1108	-0.1237	0.3156	-0.3024	-0.0068	0.1786	-0.0455	0.0094	0.1799	0.0125	0.2093	-60.0567	-28.898	39.2055
26	2.6924	-1.1067	1.1706	3.0116	-0.7783	2.1664	-0.0199	-0.0951	0.2016	0.16	-0.0849	-0.1809	-0.0215	0.0387	0.0889	0.1617	-0.0977	0.0165	0.176	-0.0157	0.1738	-52.4486	-23.1752	42.2817
27	4.409	-1.143	-0.3861	3.7659	0.1132	2.1721	0.2044	-0.6975	-0.6609	0.0891	-0.0758	0.0076	0.1657	0.1665	-0.1306	0.225	-0.09	-0.0242	0.2162	0.0276	0.238	-46.4313	-27.9547	46.6551

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 92 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 93 through 125 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 126 through 162 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 163 through 201 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 202 through 252 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 51 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 52 through 92 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 93 through 109 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 110 through 154 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 155 through 201 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 202 through 255 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 4 through 51 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 52 through 92 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 93 through 127 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 128 through 147 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 148 through 201 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 202 through 255 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 4 through 51 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 52 through 92 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 93 through 127 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 128 through 141 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 142 through 154 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 155 through 173 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 174 through 185 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 186 through 201 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 202 through 226 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 227 through 254 )

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Yorodumi