PDB-5jd4: Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrola...

ID or keywords:

Entry

Database: PDB / ID: 5jd4

Title

Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain

Components

LAE6

Keywords

HYDROLASE / alpha/beta hydrolase / esterase / metagenome / uncultured bacteria

Function / homology

Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BENZAMIDINE / Chem-PE3

Function and homology information

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Stogios, P.J. / Xu, X. / Alcaide, M. / Yim, V. / Cui, H. / Martinez-Martinez, M. / Ferrer, M. / Savchenko, A.

Citation

Journal: To Be Published
Title: Crystal structure of LAE6 Ser161Ala mutant, an alpha/beta hydrolase enzyme from the metagenome of Lake Arreo, Spain
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	Apr 26, 2017	Group: Atomic model / Structure summary
Revision 2.0	Aug 4, 2021	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1	Sep 27, 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	5jd4.cif.gz	1014.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5jd4.ent.gz	848.6 KB	Display	PDB format
PDBx/mmJSON format	5jd4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5jd4_validation.pdf.gz	926 KB	Display	wwPDB validaton report
Full document	5jd4_full_validation.pdf.gz	943.5 KB	Display
Data in XML	5jd4_validation.xml.gz	117.1 KB	Display
Data in CIF	5jd4_validation.cif.gz	168.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/5jd4 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jd4	HTTPS FTP

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Related structure data

Related structure data	1evqS 5jd3 5jd5 5jd6 S: Starting model for refinement
Similar structure data	6rb0-d 3w2l-d 1jub-d 3w2m-d 5utp-d 5mif-2 5d04-d 5tvm-1 5hc2-2 1jue-d 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

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: LAE6

B: LAE6

C: LAE6

D: LAE6

E: LAE6

F: LAE6

G: LAE6

H: LAE6

hetero molecules

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

1

A: LAE6

H: LAE6

hetero molecules

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

2

B: LAE6

E: LAE6

hetero molecules

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

3

C: LAE6

F: LAE6

hetero molecules

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

4

D: LAE6

G: LAE6

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.275, 90.098, 110.760
Angle α, β, γ (deg.)	68.02, 79.60, 67.57
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	LAE6 Mass: 36388.730 Da / Num. of mol.: 8 / Mutation: S161A 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)

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Non-polymers , 6 types, 2465 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL Mass: 634.751 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₈H₅₈O₁₅
#6: Chemical	ChemComp-BEN / BENZAMIDINE Mass: 120.152 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₇H₈N₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2409 / 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: 2.65 Å³/Da / Density % sol: 53.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M ammonium sulfate, 25% (w/v) PEG3350. Cryoprotectant: 12% glycerol and paratone-N oil.

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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: Jun 26, 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: 2.05→24.952 Å / Num. obs: 177343 / % possible obs: 94.9 % / Redundancy: 3 % / R_merge(I) obs: 0.072 / Net I/σ(I): 21.66
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.606 / Mean I/σ(I) obs: 2.52 / % possible all: 91.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1EVQ

1evq

Resolution: 2.05→24.95 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 22.87

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.211	1875	1.13 %	Random
R_work	0.169	-	-	-
obs	0.169	165467	88.3 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.05→24.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19224	0	324	2409	21957

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	20001
X-RAY DIFFRACTION	f_angle_d	0.73	27117
X-RAY DIFFRACTION	f_dihedral_angle_d	11.888	7245
X-RAY DIFFRACTION	f_chiral_restr	0.028	2879
X-RAY DIFFRACTION	f_plane_restr	0.004	3637

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 (%)
2.0497-2.1051	0.2995	111	0.2792	10492	X-RAY DIFFRACTION	74
2.1051-2.167	0.323	143	0.2483	11206	X-RAY DIFFRACTION	79
2.167-2.2369	0.2888	120	0.2267	11670	X-RAY DIFFRACTION	81
2.2369-2.3168	0.2734	142	0.2236	11881	X-RAY DIFFRACTION	83
2.3168-2.4095	0.2666	148	0.208	12280	X-RAY DIFFRACTION	87
2.4095-2.5191	0.2603	126	0.1931	12489	X-RAY DIFFRACTION	87
2.5191-2.6517	0.2368	150	0.1848	12724	X-RAY DIFFRACTION	89
2.6517-2.8177	0.2146	149	0.1736	12976	X-RAY DIFFRACTION	91
2.8177-3.0349	0.2291	153	0.1752	13112	X-RAY DIFFRACTION	92
3.0349-3.3396	0.2135	158	0.1594	13466	X-RAY DIFFRACTION	94
3.3396-3.8214	0.1805	156	0.144	13526	X-RAY DIFFRACTION	95
3.8214-4.8089	0.1701	158	0.127	13790	X-RAY DIFFRACTION	97
4.8089-24.9542	0.1758	161	0.1607	13980	X-RAY DIFFRACTION	98

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	8.6725	6.7992	-7.5175	5.6968	-6.8546	9.3047	-0.3626	-1.3324	-0.0307	0.3838	-0.0529	-0.8586	-0.2159	1.0586	0.3466	0.3244	0.1028	-0.0574	0.4425	-0.1277	0.3812	67.8775	91.8253	13.6766
2	1.9127	-0.428	0.0291	3.5898	0.0972	1.7713	-0.1147	-0.2395	-0.079	0.2674	0.1078	-0.0442	0.0768	-0.0897	0.0115	0.1692	-0.0117	0.0793	0.3195	0.0256	0.2219	50.4382	77.1759	7.8238
3	1.6362	-0.1918	-0.0502	1.5911	-0.0255	1.3172	-0.0331	-0.02	-0.195	-0.0357	0.0327	-0.157	0.1344	-0.0034	0.0044	0.1496	0.0048	0.0177	0.2058	-0.0204	0.2422	60.4785	76.4611	-3.6326
4	3.0699	-0.539	-0.7402	0.6617	-0.9945	2.9495	0.0557	0.394	0.3281	-0.5708	-0.0492	0.0321	0.099	-0.2372	-0.0067	0.4652	0.0049	-0.034	0.2345	-0.0252	0.2549	47.9677	96.4077	18.1624
5	4.9731	-4.9298	-0.4094	8.3397	1.8038	1.2185	0.0968	-0.608	-0.533	0.2092	-0.0926	0.625	0.208	-0.2986	-0.0422	0.2852	-0.1431	0.0103	0.2988	0.0456	0.3522	36.0241	85.2869	37.6551
6	1.6608	-0.1433	0.08	1.9028	0.007	1.3333	-0.0217	-0.0817	0.214	-0.0634	0.005	0.1654	-0.0584	-0.1565	0.0107	0.1802	-0.0115	-0.0005	0.1596	-0.0229	0.2244	44.2633	101.0411	36.0433
7	0.3278	0.3424	-0.7582	7.9609	2.4214	4.2909	-0.0614	-0.4716	0.3053	0.394	0.1017	0.5662	-0.053	0.0454	-0.0276	0.2116	0.0799	-0.0291	0.3859	0.0108	0.2443	103.1896	74.1444	15.7003
8	4.4752	0.3283	0.4894	9.6327	0.8876	2.0751	-0.1837	0.2424	0.1356	-0.3128	0.2319	-0.1731	-0.2753	0.436	-0.07	0.1705	-0.0585	0.0085	0.367	0.0192	0.2251	120.9167	79.6231	-4.5513
9	1.588	-0.0148	0.0948	1.3515	0.3514	1.1317	-0.0406	0.01	0.2681	-0.0854	-0.0007	0.1704	-0.1932	-0.0204	0.0356	0.1701	0.0096	-0.0253	0.2133	0.0347	0.3041	102.5133	79.2389	-3.9697
10	3.8506	-0.4562	0.4302	0.1044	0.0388	1.4802	0.0997	0.4771	-0.4279	-0.4119	-0.0812	-0.1271	-0.0434	0.0269	-0.002	0.4753	0.0059	0.0025	0.2208	0.0309	0.3011	115.0651	60.0139	18.5509
11	7.9825	-5.1593	0.4045	4.7983	-1.4208	2.2144	-0.0721	-0.4654	0.3829	0.2451	-0.0674	-0.5022	-0.1638	0.5208	0.1051	0.2618	-0.1035	-0.0337	0.3266	-0.0103	0.4674	126.8553	70.8185	37.3806
12	1.4199	0.1494	-0.4004	1.5831	0.0171	1.2866	-0.0407	-0.0968	-0.2688	-0.0078	0.004	-0.2256	0.0951	0.2	0.0273	0.1912	-0.0008	-0.0154	0.1654	0.0379	0.3095	118.6833	55.4239	36.2116
13	2.8871	-0.3419	-0.5505	2.2358	1.4465	3.8717	-0.1227	-0.5588	0.2818	0.5807	0.0854	-0.0925	0.0425	0.0049	0.0165	0.4115	0.0444	-0.0539	0.3737	-0.0424	0.2469	70.8284	96.4656	65.8931
14	4.6905	5.4215	0.0687	8.0083	-0.4504	1.528	0.2265	0.3181	-0.5065	0.0687	-0.1643	-0.6681	0.1985	0.1652	-0.1142	0.2779	0.1025	-0.0092	0.3292	-0.0888	0.3971	80.6713	84.9395	48.3604
15	1.8132	-0.5456	0.2651	1.577	-0.258	1.5584	-0.0923	-0.2344	0.4555	0.1864	0.0298	-0.3654	-0.1315	0.1795	0.0308	0.2035	-0.0082	-0.0282	0.223	-0.0666	0.3363	73.3471	101.1432	49.2019
16	2.0117	0.922	-0.1821	3.1082	-0.1479	0.8661	0.0129	0.6567	0.0038	-0.5453	-0.0065	0.5083	-0.0427	-0.0928	-0.0179	0.5202	0.0695	-0.0366	0.5552	-0.0321	0.3125	96.2233	51.3428	-32.7772
17	8.6347	6.8417	5.5941	7.1611	4.1035	9.0143	0.7075	-0.1913	-0.7745	0.5853	-0.2694	-0.9311	0.99	0.2677	-0.5283	0.3955	0.1091	-0.0418	0.2663	0.014	0.3793	108.1856	42.4701	-15.2119
18	1.584	-0.4527	-0.1211	1.8574	0.331	1.5692	0.0276	0.2266	-0.1658	-0.2262	-0.1405	0.4579	0.145	-0.1619	0.0689	0.2214	0.0039	-0.0753	0.2584	-0.0206	0.3283	91.2986	52.3712	-17.1912
19	6.2567	0.6736	-0.9994	0.1184	0.0378	3.1151	-0.051	-1.0808	-0.745	0.5516	0.0267	0.15	0.1911	0.0095	0.0314	0.6333	0.0471	0.0261	0.549	0.0729	0.3588	94.2082	58.073	69.0059
20	5.6506	1.5184	2.2158	5.3387	1.7625	3.068	-0.1605	-0.0785	-0.0519	0.1808	-0.16	0.4767	-0.2547	-0.3646	0.286	0.251	0.0757	0.0306	0.2329	-0.0017	0.3511	81.8381	72.2847	48.6605
21	1.8427	-0.4376	-0.4831	1.8854	0.3132	1.6336	-0.0865	-0.2216	-0.3792	0.2661	-0.0329	0.4075	0.1523	-0.2013	0.0588	0.2373	-0.0202	0.0558	0.2172	0.0524	0.3587	89.6474	55.3224	49.5487
22	1.0915	0.2103	-0.4532	2.564	0.6277	2.1571	0.2191	0.633	0.1643	-0.764	-0.1966	-0.4972	0.0164	-0.0109	-0.0621	0.565	0.1377	0.1081	0.5618	0.0644	0.3402	66.3273	104.1133	-32.7426
23	7.6574	5.1027	-2.9453	6.663	-0.5045	8.3821	0.666	0.1022	1.1521	0.277	-0.055	1.0639	-0.9815	-0.3657	-0.6466	0.3337	0.1156	0.0702	0.2418	0.0151	0.4011	54.6205	113.0435	-15.3595
24	1.4393	-0.3935	0.0068	2.1079	-0.2503	1.4105	0.0596	0.2409	0.2508	-0.2829	-0.1173	-0.5972	-0.1319	0.1747	0.0204	0.2276	0.0068	0.0905	0.2599	0.04	0.4019	71.4672	103.229	-17.2303

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID -1:12)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 13:77)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 78:315)
4	X-RAY DIFFRACTION	4	(CHAIN B AND RESID -1:55)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 56:78)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 79:315)
7	X-RAY DIFFRACTION	7	(CHAIN C AND RESID -1:49)
8	X-RAY DIFFRACTION	8	(CHAIN C AND RESID 50:77)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 78:315)
10	X-RAY DIFFRACTION	10	(CHAIN D AND RESID -1:56)
11	X-RAY DIFFRACTION	11	(CHAIN D AND RESID 57:77)
12	X-RAY DIFFRACTION	12	(CHAIN D AND RESID 78:315)
13	X-RAY DIFFRACTION	13	(CHAIN E AND RESID -1:60)
14	X-RAY DIFFRACTION	14	(CHAIN E AND RESID 61:77)
15	X-RAY DIFFRACTION	15	(CHAIN E AND RESID 78:315)
16	X-RAY DIFFRACTION	16	(CHAIN F AND RESID -1:65)
17	X-RAY DIFFRACTION	17	(CHAIN F AND RESID 66:77)
18	X-RAY DIFFRACTION	18	(CHAIN F AND RESID 78:315)
19	X-RAY DIFFRACTION	19	(CHAIN G AND RESID -1:49)
20	X-RAY DIFFRACTION	20	(CHAIN G AND RESID 50:78)
21	X-RAY DIFFRACTION	21	(CHAIN G AND RESID 79:315)
22	X-RAY DIFFRACTION	22	(CHAIN H AND RESID -1:65)
23	X-RAY DIFFRACTION	23	(CHAIN H AND RESID 66:77)
24	X-RAY DIFFRACTION	24	(CHAIN H AND RESID 78:315)

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Protein , 1 types, 8 molecules ABCDEFGH

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Non-polymers , 6 types, 2465 molecules

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-Protein , 1 types, 8 molecules ABCDEFGH

-Non-polymers , 6 types, 2465 molecules

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Protein , 1 types, 8 molecules ABCDEFGH

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Non-polymers , 6 types, 2465 molecules

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi