PDB-4c89: Crystal structure of carboxylesterase LpEst1 from Lactobacillus p...

ID or keywords:

Entry

Database: PDB / ID: 4c89

Title

Crystal structure of carboxylesterase LpEst1 from Lactobacillus plantarum: high resolution model

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 /

MOLECULAR REPLACEMENT / Resolution: 2.05 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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PDBx/mmCIF format	4c89.cif.gz	576.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4c89.ent.gz	477.6 KB	Display	PDB format
PDBx/mmJSON format	4c89.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4c89_validation.pdf.gz	472.6 KB	Display	wwPDB validaton report
Full document	4c89_full_validation.pdf.gz	479.7 KB	Display
Data in XML	4c89_validation.xml.gz	78.2 KB	Display
Data in CIF	4c89_validation.cif.gz	116.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/4c89 ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c89	HTTPS FTP

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Related structure data

Related structure data	4c87C 4c88C C: citing same article (ref.)
Similar structure data	4c87-1 4c88-1 3a65-1 4o89-d 3nnf-1 2e8i-2 2zm9-1 4c87-2 3vwm-1 7cju-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

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

1

A: ESTERASE

C: ESTERASE

hetero molecules

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

2

B: ESTERASE

D: ESTERASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	168.790, 168.790, 184.570
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 / 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.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2196 / 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: 4.41 Å³/Da / Density % sol: 72.1 % / 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: ID14-4 / Wavelength: 0.97914
Detector	Type: ADSC QUANTUM 315r / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection twin	Operator: -H,K,-L / Fraction: 0.2
Reflection	Resolution: 2.05→53 Å / Num. obs: 161172 / % possible obs: 100 % / Redundancy: 7.5 % / B_iso Wilson estimate: 22.9 Å² / R_merge(I) obs: 0.14 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.05→2.16 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.05→53.376 Å / σ(F): 1.35 / Phase error: 18.47 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.1425	8079	5 %
R_work	0.1224	-	-
obs	0.1238	161172	100 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→53.376 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10481	0	44	2196	12721

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10917
X-RAY DIFFRACTION	f_angle_d	1.025	14990
X-RAY DIFFRACTION	f_dihedral_angle_d	14.531	3864
X-RAY DIFFRACTION	f_chiral_restr	0.068	1725
X-RAY DIFFRACTION	f_plane_restr	0.005	1990

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 (%)
2.0502-2.0856	0.2251	382	0.2101	7669	X-RAY DIFFRACTION	95
2.0856-2.1235	0.2147	411	0.1944	7688	X-RAY DIFFRACTION	95
2.1235-2.1643	0.1959	390	0.1789	7579	X-RAY DIFFRACTION	95
2.1643-2.2085	0.1881	425	0.1757	7607	X-RAY DIFFRACTION	95
2.2085-2.2565	0.1698	405	0.1633	7668	X-RAY DIFFRACTION	95
2.2565-2.3089	0.1746	434	0.153	7556	X-RAY DIFFRACTION	95
2.3089-2.3666	0.1754	439	0.1514	7589	X-RAY DIFFRACTION	95
2.3666-2.4306	0.1677	394	0.1491	7705	X-RAY DIFFRACTION	95
2.4306-2.5021	0.1689	422	0.146	7566	X-RAY DIFFRACTION	95
2.5021-2.5828	0.1661	400	0.1443	7619	X-RAY DIFFRACTION	95
2.5828-2.675	0.1732	404	0.1401	7657	X-RAY DIFFRACTION	95
2.675-2.782	0.1646	388	0.1303	7677	X-RAY DIFFRACTION	95
2.782-2.9085	0.1395	371	0.1254	7706	X-RAY DIFFRACTION	95
2.9085-3.0617	0.136	413	0.1218	7589	X-RAY DIFFRACTION	95
3.0617-3.2532	0.125	413	0.1145	7640	X-RAY DIFFRACTION	95
3.2532-3.504	0.1242	379	0.1063	7699	X-RAY DIFFRACTION	95
3.504-3.8558	0.1117	419	0.0934	7647	X-RAY DIFFRACTION	95
3.8558-4.4118	0.1134	381	0.0826	7705	X-RAY DIFFRACTION	95
4.4118-5.5513	0.113	406	0.0872	7678	X-RAY DIFFRACTION	95
5.5513-27.9306	0.132	403	0.1192	7751	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	1.4574	0.9465	-0.7826	2.0186	-0.6596	1.4243	0.0528	-0.0684	0.0846	-0.0247	-0.0573	-0.1974	-0.2009	0.2837	0.0194	0.1942	-0.0468	-0.0187	0.2105	0.0304	0.186	-38.7517	-40.2547	7.5549
2	2.6656	0.2016	0.7801	0.944	0.1948	1.1991	0.0032	-0.3018	-0.0044	0.0972	0.0098	0.0208	-0.0607	0.01	-0.0079	0.1602	-0.0253	0.017	0.1722	0.0216	0.126	-51.3461	-46.168	26.1825
3	1.3235	-0.0257	-0.7823	0.3291	-0.0201	0.9789	0.0119	-0.0068	0.109	-0.0338	0.0155	-0.0114	-0.0694	-0.007	-0.0303	0.1711	-0.0271	0.0054	0.1584	0.0267	0.1443	-55.3965	-40.2527	11.7755
4	2.2632	0.3224	-0.0734	0.6664	0.1858	1.1089	0.0194	0.0274	0.2439	-0.0253	0.0107	0.0123	-0.2328	-0.0489	-0.0235	0.1948	-0.0173	0.0241	0.1239	0.0296	0.1562	-51.5698	-35.1224	11.2713
5	1.8488	-0.0741	-0.0864	0.7733	-0.4642	2.4127	0.0109	0.0861	0.1087	0.0207	0.1103	0.1708	-0.1427	-0.3413	-0.1592	0.1884	-0.0414	0.0208	0.1505	0.008	0.1686	-45.4799	-36.5357	-29.9203
6	1.8515	-1.191	-0.7512	1.5965	0.7901	1.3809	0.0582	0.0289	0.2642	-0.0316	-0.006	-0.2088	-0.1602	0.0618	-0.0556	0.1536	-0.0547	0.0264	0.1469	0.0417	0.1718	-24.5343	-25.6586	-27.2796
7	1.7599	0.0812	0.1923	0.5539	-0.0652	0.708	0.0067	0.0236	-0.0378	-0.0099	-0.0212	-0.0358	0.074	-0.0062	0.0143	0.1684	-0.0398	0.0294	0.1653	0.0255	0.1526	-28.3501	-41.1907	-28.9045
8	1.2518	-0.1444	-0.3114	0.3433	0.0885	0.8315	-0.0542	0.0111	-0.0956	0.0334	0.0411	-0.001	0.0614	-0.035	0.0266	0.1785	-0.0485	0.0177	0.167	0.0233	0.1652	-33.1186	-41.8942	-24.6967
9	1.4512	0.788	-0.9153	2.2623	-0.3693	3.7541	0.0376	0.0557	0.1618	-0.08	-0.0231	-0.1123	-0.3152	0.1945	-0.0649	0.1013	0.0141	-0.0014	0.181	0.0137	0.1849	-28.8224	-65.033	21.3621
10	0.5982	-0.5059	0.168	3.901	-1.3061	1.4747	-0.0112	0.0314	-0.0009	-0.0606	0.0319	0.3557	0.0374	-0.0746	-0.0427	0.1363	-0.0114	0.0249	0.1538	-0.0153	0.1956	-49.6598	-76.8029	17.9146
11	0.9371	0.6605	0.3164	1.6701	0.4797	0.9811	-0.0282	0.0289	-0.0058	-0.0557	0.0217	-0.0884	0.0252	0.1446	0.0017	0.1454	0.0076	0.0326	0.1653	0.0032	0.1634	-34.3981	-81.5967	19.4823
12	0.2898	0.145	0.1184	2.1696	-0.2309	0.7993	0.0023	0.0991	-0.0518	-0.1923	0.0099	-0.1575	0.0599	0.1277	0.0009	0.1354	-0.0055	0.0389	0.2083	-0.0094	0.1742	-31.3206	-77.8309	15.245
13	2.9028	-0.1998	-0.9136	1.7775	-0.0815	1.3525	-0.179	-0.0938	-0.3241	0.3421	0.0829	0.5014	0.306	-0.3545	0.097	0.3656	-0.0381	0.1317	0.3016	-0.0072	0.3281	-61.4973	-15.9641	-16.7862
14	1.7761	0.7972	0.916	2.2598	0.5991	1.4233	-0.0443	0.0477	0.0128	-0.1274	0.0598	0.0842	-0.0282	-0.0928	-0.0133	0.1602	0.0102	0.0428	0.18	0.0035	0.1638	-49.7614	-8.3806	-35.55
15	0.8508	0.1411	-0.0855	1.5472	0.356	0.8042	-0.0297	-0.179	0.0306	0.3087	-0.0107	0.2669	0.1236	-0.1644	-0.0426	0.2197	0.0122	0.0811	0.213	-0.0112	0.1858	-52.8639	-1.713	-21.1716
16	1.2618	0.5034	0.1954	1.6069	0.2517	0.7114	-0.0181	-0.1469	0.1115	0.2935	-0.0711	0.449	-0.0283	-0.2365	0.0918	0.235	0.0246	0.1134	0.2936	-0.0136	0.2781	-59.2282	-2.3829	-20.7356

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID -3 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 -3 THROUGH 58 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 59 THROUGH 146 )
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESID 147 THROUGH 249 )
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESID 250 THROUGH 337 )
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID -1 THROUGH 58 )
10	X-RAY DIFFRACTION	10	CHAIN C AND (RESID 59 THROUGH 146 )
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESID 147 THROUGH 249 )
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESID 250 THROUGH 337 )
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESID -3 THROUGH 58 )
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESID 59 THROUGH 146 )
15	X-RAY DIFFRACTION	15	CHAIN D AND (RESID 147 THROUGH 249 )
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESID 250 THROUGH 337 )

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