PDB-4c87: Esterase LpEst1 from Lactobacillus plantarum WCFS1

ID or keywords:

Entry

Database: PDB / ID: 4c87

Title

Esterase LpEst1 from Lactobacillus plantarum WCFS1

Components

ESTERASE

Keywords

HYDROLASE

Function / homology

Function and homology information

carboxylesterase / carboxylesterase activity / hydrolase activity
Similarity search - Function

Biological species

LACTOBACILLUS PLANTARUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.65 Å

Authors

Alvarez, Y. / Esteban-Torres, M. / Cortes-Cabrera, A. / Gago, F. / Acebron, I. / Benavente, R. / Mardo, K. / de-las-Rivas, B. / Munoz, R. / Mancheno, J.M.

Citation

Journal: Plos One / Year: 2014
Title: Esterase Lpest1 from Lactobacillus Plantarum: A Novel and Atypical Member of the Alpha Beta Hydrolase Superfamily of Enzymes
Authors: Alvarez, Y. / Esteban-Torres, M. / Cortes-Cabrera, A. / Gago, F. / Acebron, I. / Benavente, R. / Mardo, K. / De-Las-Rivas, B. / Munoz, R. / Mancheno, J.M.

History

Deposition	Sep 30, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 2, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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	4c87.cif.gz	545.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4c87.ent.gz	454.7 KB	Display	PDB format
PDBx/mmJSON format	4c87.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c87_validation.pdf.gz	480.5 KB	Display	wwPDB validaton report
Full document	4c87_full_validation.pdf.gz	493.1 KB	Display
Data in XML	4c87_validation.xml.gz	65.5 KB	Display
Data in CIF	4c87_validation.cif.gz	88.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/4c87 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c87	HTTPS FTP

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Related structure data

Related structure data	4c88C 4c89C C: citing same article (ref.)
Similar structure data	4c89-1 4c89-2 2zly-1 5b80-d 1c3r-d 2cmu-1 3vwp-1 4l00-d 3r4y-d 3r4z-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) 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

Deposited unit

A: ESTERASE

B: ESTERASE

C: ESTERASE

D: ESTERASE

hetero molecules

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

1

A: ESTERASE

B: ESTERASE

hetero molecules

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

2

C: ESTERASE

D: ESTERASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	168.340, 168.340, 184.200
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

#1: Protein	ESTERASE / CARBOXYLESTERASE LPEST1 Mass: 38985.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOBACILLUS PLANTARUM (bacteria) / Strain: WCFS1 / Plasmid: PURI3-TEV-LPEST1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q88Y25, UniProt: F9UMG7*PLUS, carboxylesterase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 823 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 4.44 Å³/Da / Density % sol: 72.3 % / Description: NONE
Crystal grow	pH: 7 Details: 1 M SODIUM MALONATE, 0.5 % (V/V) JEFFAMINE ED-2001, 100 MM HEPES PH 7.0, 5 MM DTT

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97915
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.65→47 Å / Num. obs: 75273 / % possible obs: 100 % / Redundancy: 13.9 % / B_iso Wilson estimate: 47.8 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 25.8
Reflection shell	Resolution: 2.65→2.79 Å / Redundancy: 13.1 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.65→53.234 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 17.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1825	3736	5 %
R_work	0.1491	-	-
obs	0.1508	74240	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→53.234 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10417	0	102	823	11342

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10940
X-RAY DIFFRACTION	f_angle_d	1.049	14998
X-RAY DIFFRACTION	f_dihedral_angle_d	15.196	3922
X-RAY DIFFRACTION	f_chiral_restr	0.076	1721
X-RAY DIFFRACTION	f_plane_restr	0.005	1982

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 (%)
2.6501-2.6836	0.2492	147	0.204	2640	X-RAY DIFFRACTION	100
2.6836-2.7189	0.2365	142	0.184	2553	X-RAY DIFFRACTION	100
2.7189-2.7562	0.2229	135	0.1819	2641	X-RAY DIFFRACTION	100
2.7562-2.7956	0.2424	132	0.1766	2601	X-RAY DIFFRACTION	100
2.7956-2.8373	0.2292	121	0.1791	2635	X-RAY DIFFRACTION	100
2.8373-2.8816	0.2315	143	0.1763	2566	X-RAY DIFFRACTION	100
2.8816-2.9289	0.2001	159	0.1726	2591	X-RAY DIFFRACTION	100
2.9289-2.9794	0.2293	140	0.178	2581	X-RAY DIFFRACTION	100
2.9794-3.0335	0.2371	134	0.1702	2608	X-RAY DIFFRACTION	100
3.0335-3.0919	0.1892	148	0.1738	2628	X-RAY DIFFRACTION	100
3.0919-3.155	0.217	138	0.1591	2569	X-RAY DIFFRACTION	100
3.155-3.2236	0.2002	130	0.1598	2623	X-RAY DIFFRACTION	100
3.2236-3.2985	0.1859	130	0.1568	2619	X-RAY DIFFRACTION	100
3.2985-3.381	0.1944	124	0.1592	2622	X-RAY DIFFRACTION	100
3.381-3.4724	0.1701	146	0.1474	2583	X-RAY DIFFRACTION	100
3.4724-3.5746	0.1647	135	0.1331	2635	X-RAY DIFFRACTION	100
3.5746-3.6899	0.1602	150	0.1263	2584	X-RAY DIFFRACTION	100
3.6899-3.8218	0.1733	130	0.1228	2615	X-RAY DIFFRACTION	100
3.8218-3.9748	0.1404	161	0.1249	2595	X-RAY DIFFRACTION	100
3.9748-4.1556	0.1541	116	0.1176	2636	X-RAY DIFFRACTION	100
4.1556-4.3746	0.1474	143	0.1122	2593	X-RAY DIFFRACTION	100
4.3746-4.6485	0.1333	143	0.1138	2616	X-RAY DIFFRACTION	100
4.6485-5.0072	0.1422	140	0.1173	2621	X-RAY DIFFRACTION	100
5.0072-5.5106	0.1656	130	0.1318	2627	X-RAY DIFFRACTION	100
5.5106-6.3069	0.1841	139	0.1556	2624	X-RAY DIFFRACTION	100
6.3069-7.9418	0.1965	139	0.163	2646	X-RAY DIFFRACTION	100
7.9418-53.2445	0.1952	141	0.1937	2652	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	0.6956	-0.1162	0.4915	0.6858	0.145	1.2116	0.0059	-0.0749	-0.3038	0.029	-0.0954	-0.2201	0.0884	0.0507	-0.2584	0.161	0.004	-0.0803	0.1774	0.0621	0.082	55.5471	148.8467	-73.2783
2	0.2682	0.0847	0.379	1.1374	-0.1556	0.7229	0.0532	-0.2336	0.0436	-0.0537	-0.1806	0.4506	0.1374	-0.4134	-0.2109	0.0586	0.1243	-0.0645	-0.0851	0.0219	0.2104	34.6786	160.6799	-69.9938
3	0.5262	-0.2223	0.3139	1.2483	0.1276	0.4479	-0.0469	-0.0937	-0.0022	0.0384	0.065	-0.0684	-0.0857	0.2122	0.018	0.0534	0.0005	-0.0258	0.0872	0.001	0.1091	49.7669	165.5928	-71.2105
4	0.6171	-0.7401	-0.1364	1.1382	-0.3668	0.8598	-0.0527	-0.1043	0.0439	0.2414	0.0388	-0.2151	-0.0881	0.1274	0.0144	0.0958	0.0094	-0.0703	0.1422	-0.0032	0.1325	52.9816	161.7585	-67.2024
5	0.9104	-0.04	0.3246	1.6073	0.8423	1.2303	0.1128	0.1529	-0.1814	-0.115	0.1787	-0.1578	0.1892	0.3258	0.1646	0.19	0.1029	-0.016	0.1553	0.0588	0.1601	48.9088	118.1897	-59.1068
6	0.9359	-0.2233	0.0077	0.4053	0.117	0.8176	0.1123	0.2807	0.4359	-0.1288	0.2825	-0.1955	-0.0998	-0.0255	0.2497	0.0544	0.0305	-0.0195	0.0745	0.0164	0.1018	36.1037	137.2183	-70.8536
7	1.3377	-0.1976	-0.4463	0.6689	-0.1336	0.557	-0.0209	0.2879	0.0376	-0.2869	0.0114	0.0699	-0.0152	-0.1057	0.0384	0.0862	0.0202	-0.052	0.1415	-0.0034	0.0771	31.6031	128.9655	-77.252
8	0.9676	-0.0617	0.5214	0.4274	-0.2858	0.3579	0.015	-0.0959	-0.1364	-0.0093	-0.0404	-0.0321	0.2189	-0.1391	-0.0604	0.0772	0.0467	-0.027	0.1268	0.0366	0.0871	28.959	124.2494	-63.9231
9	2.5759	-0.9743	-0.0175	1.1581	-0.2775	0.9694	-0.0484	-0.1883	-0.1974	-0.0288	0.0587	0.1081	0.2771	-0.2289	0.0053	0.1056	-0.0207	-0.0174	0.1278	0.0075	0.0931	24.6525	120.6714	-60.5197
10	1.0074	0.1736	0.1899	0.5933	-0.0763	0.8148	-0.0709	0.0272	-0.236	0.0545	0.1488	-0.0527	0.1358	0.0425	-0.0245	0.1633	0.0741	-0.0307	0.0886	0.0242	0.1322	39.2366	118.1973	-65.1044
11	0.5059	-0.0268	0.8212	0.6564	0.2237	3.2014	-0.1815	0.0675	0.0483	0.0512	-0.0441	-0.3018	-0.3943	0.6262	-0.7593	0.0665	0.072	0.0944	0.1588	-0.0434	0.0698	49.2869	130.7338	-119.513
12	0.402	0.1798	-0.3504	0.437	-0.0811	0.2916	0.0428	-0.2886	0.1408	0.1618	-0.2226	0.1199	-0.2092	0.0406	-0.1439	0.1232	0.0406	0.032	0.2297	-0.0893	0.0788	29.7801	141.5297	-106.897
13	0.9221	0.329	-0.2265	0.6283	0.4232	0.8297	-0.0976	-0.0734	0.3541	-0.3289	-0.038	0.2576	-0.4783	-0.2782	-0.3633	-0.0864	0.1442	0.0359	0.1073	-0.0735	0.0983	23.8683	140.9271	-117.3302
14	1.2048	0.2121	-0.2126	0.4855	0.4051	0.3972	-0.0303	0.1677	-0.0248	-0.0254	0.0035	0.1497	0.0481	-0.1092	0.0135	0.0778	0.0566	0.0115	0.1253	-0.003	0.0812	24.4169	128.5684	-119.7114
15	3.2137	-0.4076	0.104	0.4084	0.1132	0.0925	0.0542	0.0426	-0.2727	0.2401	-0.0042	-0.0083	0.313	0.0744	-0.0205	0.121	0.0843	-0.0259	0.2172	-0.0134	0.0979	38.6392	123.8165	-103.3766
16	1.6342	0.022	-0.7168	0.5862	-0.3489	0.7666	-0.0021	0.004	-0.2343	-0.1184	0.0844	0.0905	0.112	-0.0423	0.0281	0.1075	0.0338	0.0114	0.1252	-0.0718	0.0991	26.5657	121.1919	-116.7485
17	0.8591	0.1399	0.0595	0.6631	0.0939	0.4459	-0.0563	0.0973	0.0126	-0.052	0.0693	-0.0185	-0.0244	0.0718	0.0038	0.0672	0.0496	0.0083	0.1343	-0.037	0.0921	37.6259	130.0417	-121.5712
18	1.01	0.1302	0.1128	0.1559	-0.3064	1.0843	0.0196	0.032	-0.178	-0.3539	-0.0187	-0.4745	0.5227	0.48	0.164	0.2354	0.0831	0.2435	0.2323	-0.087	0.5123	68.2571	152.6791	-127.9183
19	0.885	0.0185	0.0186	0.8513	0.0501	0.2888	0.0683	0.0369	-0.1637	-0.0411	0.0476	0.0032	0.0551	-0.0103	-0.0053	0.153	0.0154	0.028	0.1277	-0.0314	0.0867	45.4305	153.6272	-116.0854
20	1.2459	-0.3235	0.4047	0.9826	-0.583	1.0293	-0.0298	-0.062	0.0253	0.1539	0.0241	-0.085	-0.0246	0.0327	-0.0248	0.1131	0.0007	-0.0067	0.0752	-0.0296	0.0954	50.1207	161.6781	-109.5339
21	0.9152	-0.0233	-0.2576	1.2111	-0.3843	0.7593	0.0077	0.1879	0.2228	-0.4211	0.0526	-0.4372	0.1614	0.185	-0.0264	0.2314	0.0109	0.1165	0.1041	0.0122	0.0465	52.7042	166.5174	-123.0763
22	2.2507	-0.5646	0.0276	0.8486	-0.0813	0.9743	-0.0392	0.1098	0.2837	-0.4337	0.0038	-0.3248	-0.3196	0.1944	-0.0261	0.2299	-0.0584	0.0835	0.1202	-0.0041	0.2034	53.5901	172.0645	-126.1639
23	0.3851	0.1393	-0.1984	0.4772	0.0315	0.5134	0.0236	0.1453	0.0618	-0.2658	0.034	-0.6533	0.0802	0.2839	0.009	0.1335	-0.0017	0.2155	0.2101	-0.0023	0.3253	63.3174	160.8516	-121.6891

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID -1 THROUGH 58 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 59 THROUGH 146 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 147 THROUGH 249 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 250 THROUGH 337 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 0 THROUGH 42 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 43 THROUGH 80 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 81 THROUGH 146 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 147 THROUGH 249 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 250 THROUGH 285 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 286 THROUGH 337 )
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID -1 THROUGH 42 )
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESID 43 THROUGH 80 )
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESID 81 THROUGH 146 )
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESID 147 THROUGH 224 )
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESID 225 THROUGH 249 )
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESID 250 THROUGH 285 )
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESID 286 THROUGH 337 )
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESID 0 THROUGH 42 )
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESID 43 THROUGH 80 )
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESID 81 THROUGH 146 )
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESID 147 THROUGH 249 )
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESID 250 THROUGH 285 )
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESID 286 THROUGH 337 )

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