PDB-5l2p: Structure of arylesterase

ID or keywords:

Entry

Database: PDB / ID: 5l2p

Title

Structure of arylesterase

Components

Arylesterase

Keywords

HYDROLASE / arylesterase

Function / homology

Function and homology information

arylesterase / aryldialkylphosphatase / aryldialkylphosphatase activity / arylesterase activity
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.56 Å

Authors

Lee, H.B. / Park, Y.J.

Citation

Journal: To Be Published
Title: Structure of arylesterase
Authors: Lee, H.B. / Park, Y.J.

History

Deposition	Aug 2, 2016	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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	5l2p.cif.gz	480.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5l2p.ent.gz	401.5 KB	Display	PDB format
PDBx/mmJSON format	5l2p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l2/5l2p ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l2p	HTTPS FTP

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Related structure data

Related structure data	3aimS S: Starting model for refinement
Similar structure data	1ek2-d 3wj1-1 1y4u-d 5y1b-2 3ozp-1 3852 4gop-1 3wj2-d 4qcl-d 1cqz-d 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: Arylesterase

B: Arylesterase

C: Arylesterase

D: Arylesterase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	73.913, 109.309, 90.044
Angle α, β, γ (deg.)	90.000, 109.370, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Arylesterase / A-esterase / Paraoxonase Mass: 34590.754 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: are Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: B5BLW5, arylesterase, aryldialkylphosphatase

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 70%(V/V) MPD

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2015

Radiation

Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 2.56→60 Å / Num. obs: 40400 / % possible obs: 94.5 % / Redundancy: 2.8 % / R_merge(I) obs: 0.141 / Net I/av σ(I): 7.514 / Net I/σ(I): 7.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
2.6-2.64	1.8	0.411	0.679	1	79.6
2.64-2.69	1.9	0.377	0.772	1	84
2.69-2.74	2	0.363	0.74	1	86.1
2.74-2.8	2.1	0.367	0.77	1	89.7
2.8-2.86	2.3	0.345	0.816	1	91.8
2.86-2.93	2.4	0.386	0.786	1	94.1
2.93-3	2.3	0.356	0.797	1	92.7
3-3.08	2.8	0.397	0.756	1	96.3
3.08-3.17	3	0.349	0.829	1	98
3.17-3.28	3.1	0.289	0.867	1	98.5
3.28-3.39	3.2	0.255	0.882	1	98.6
3.39-3.53	3.2	0.28	0.306	1	97.6
3.53-3.69	3.2	0.187	0.933	1	98.4
3.69-3.88	3	0.158	0.959	1	96.3
3.88-4.13	3.2	0.13	0.963	1	97.8
4.13-4.45	3.4	0.102	0.98	1	99
4.45-4.89	3.3	0.099	0.974	1	98.9
4.89-5.6	3.2	0.093	0.985	1	96.9
5.6-7.05	3.3	0.092	0.977	1	97.4
7.05-60	3.3	0.121	0.966	1	98

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	8.48 Å	56.26 Å
Translation	8.48 Å	56.26 Å

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Processing

Software

Name	Version	Classification
DENZO		data collection
SCALEPACK		data reduction
PHASER	2.5.1	phasing
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3AIM

3aim

Resolution: 2.56→50 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.929 / SU B: 25.393 / SU ML: 0.241 / SU R Cruickshank DPI: 0.3342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.31
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2305	2029	5 %	RANDOM
R_work	0.216	-	-	-
obs	0.2168	38349	92.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 116.72 Å² / B_iso mean: 57.988 Å² / B_iso min: 31.94 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.28 Å²	0 Å²	-0.34 Å²
2-	-	-3.92 Å²	0 Å²
3-	-	-	7.47 Å²

Refinement step

Cycle: final / Resolution: 2.56→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9684	0	0	0	9684
Num. residues	-	-	-	-	1218

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	9894
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9781
X-RAY DIFFRACTION	r_angle_refined_deg	1.347	1.977	13427
X-RAY DIFFRACTION	r_angle_other_deg	0.754	3.001	22230
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.275	5	1213
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.009	23.889	450
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.622	15	1703
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.919	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	1508
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11116
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2232

LS refinement shell

Resolution: 2.562→2.628 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.307	89	-
R_work	0.323	1875	-
all	-	1964	-
obs	-	-	61.15 %

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	4.9298	1.0304	-1.0543	7.4705	-2.8113	8.4414	0.1274	-0.0492	-0.0434	-0.2352	-0.1557	0.1136	0.3067	0.5991	0.0283	0.3666	0.0268	0.0704	0.3892	-0.0537	0.2032	45.2599	6.0515	78.3229
2	3.4837	0.5742	-0.1059	1.7166	-0.2306	1.4715	-0.0738	0.1656	-0.0153	-0.3085	0.0108	-0.1338	-0.0464	0.0729	0.063	0.508	0.0175	0.0322	0.3912	-0.0263	0.0974	26.262	15.9618	67.3933
3	2.1685	0.3759	0.862	2.6971	0.3874	0.7772	0.0245	0.2236	0.0221	-0.0956	-0.0452	0.1049	-0.1965	-0.0687	0.0207	0.4187	0.0271	0.0418	0.3406	-0.0029	0.0557	20.4575	18.8486	74.8171
4	2.7914	0.2482	0.918	1.2622	0.01	1.3318	0.0311	0.2067	0.1239	-0.1309	-0.0807	0.0716	-0.1612	-0.0703	0.0497	0.3899	0.0224	0.0414	0.2873	-0.0182	0.0758	26.8955	19.7631	85.4961
5	0.3662	-1.4593	0.5127	6.0966	-1.3682	5.9155	-0.0896	0.0127	0.0502	0.2158	0.1726	-0.1136	-0.6657	0.1568	-0.083	0.4286	0.0037	-0.0088	0.3243	0.0073	0.2355	31.7822	31.878	85.8094
6	8.9786	-2.1984	-2.2553	3.3775	0.2439	0.8189	0.0237	-0.1157	0.1189	0.1582	-0.0037	0.1713	-0.1803	-0.1395	-0.02	0.3599	-0.0096	0.0412	0.3368	-0.044	0.0305	25.7476	16.864	94.12
7	4.1876	0.2724	0.8433	1.4297	-0.5661	0.507	0.0299	0.2773	-0.2912	0.0066	0.0657	0.1352	-0.0922	-0.0713	-0.0956	0.3947	0.0437	0.0408	0.3153	-0.0636	0.085	25.628	5.0214	84.9193
8	1.1874	2.876	-3.0302	10.2734	-2.0524	16.1963	-0.0721	0.0687	0.0039	-0.2537	0.2011	-0.0681	0.0597	-0.06	-0.129	0.4199	0.0572	0.0598	0.3313	-0.0099	0.2827	23.2924	11.4093	106.4357
9	9.8213	-1.9316	0.5632	0.6206	-1.5404	12.0389	-0.1837	-0.4235	0.2058	0.2034	0.1522	0.0795	-0.3481	-0.2234	0.0315	0.4464	-0.0061	0.1375	0.4174	0.0172	0.2632	19.8349	4.8113	116.3213
10	1.1579	0.1729	0.7341	2.0157	0.5117	3.3793	0.008	-0.219	-0.2077	0.2877	0.0568	0.0144	0.1242	-0.2202	-0.0648	0.3193	-0.0334	0.1198	0.4404	0.0107	0.1832	14.3572	-14.8787	106.1232
11	1.6226	-0.5185	1.5883	0.973	0.0156	2.0659	0.0218	-0.0406	-0.1193	0.02	0.0742	0.0543	0.0512	-0.0768	-0.096	0.3254	-0.049	0.1236	0.3388	0.0072	0.1511	20.7113	-17.5783	99.2883
12	1.4246	0.0639	0.2404	0.9524	-0.2503	0.3395	0.0345	-0.0346	-0.1403	0.0127	-0.0596	0.1336	0.1312	-0.0686	0.025	0.3247	-0.023	0.1068	0.2985	-0.0059	0.0838	31.0064	-10.6778	99.8126
13	3.0952	2.1977	-1.3313	2.6095	0.2317	10.8901	0.0705	-0.313	-0.3821	0.2141	-0.225	0.0046	0.0357	0.2664	0.1545	0.3198	0.0294	0.0418	0.289	0.0757	0.1381	38.5431	-16.4208	109.0311
14	0.7607	0.5306	0.233	1.5427	0.9357	1.6484	-0.0495	0.0312	-0.1447	-0.1687	-0.0444	0.1098	-0.1464	0.0193	0.0938	0.312	-0.0094	0.0966	0.2986	0.0059	0.1104	28.9165	-2.9088	94.3328
15	2.8623	-1.3099	-1.9754	10.1144	1.6166	2.8537	0.1117	0.461	0.1162	-0.1608	-0.04	-0.3422	0.0891	-0.2513	-0.0717	0.4735	-0.0178	0.0559	0.4274	-0.0379	0.1881	61.8137	7.8181	90.2284
16	4.5883	2.9315	0.1392	9.0305	2.6035	8.7591	0.1547	0.4157	-0.0196	-0.269	-0.2906	-0.3296	0.0521	-0.1242	0.1359	0.3702	-0.0028	0.0549	0.4254	-0.0055	0.0272	72.6783	-4.3972	98.0083
17	2.2659	1.2666	-0.0512	8.9322	-1.8374	2.0093	0.0034	-0.1312	0.0917	0.1486	-0.1583	-0.4723	0.0089	0.11	0.1549	0.2822	0.0113	0.0777	0.3815	-0.0308	0.1022	77.4506	2.5782	117.901
18	1.2507	0.1911	0.7306	2.7344	1.0803	1.9516	-0.0007	-0.0212	0.0135	0.0386	0.0414	-0.2032	-0.0123	0.0666	-0.0407	0.2845	0.0262	0.0907	0.2788	0.0388	0.061	69.0307	-0.79	116.2354
19	2.2448	0.1717	1.3313	0.9075	-0.0695	2.0973	0.0681	-0.0474	-0.0979	0.1075	-0.0246	-0.0993	0.2359	-0.0307	-0.0435	0.3037	0.0353	0.0962	0.23	-0.0196	0.0691	57.1949	0.085	113.348
20	4.6007	-1.8233	0.2901	5.3159	1.7343	1.975	0.0618	0.4212	-0.2468	0.0601	-0.0772	-0.0865	0.3291	-0.1632	0.0153	0.3797	-0.0198	0.1057	0.2878	-0.0179	0.189	53.4361	-12.3201	110.2092
21	1.7177	-0.1031	0.457	0.5895	0.1256	2.3765	-0.0547	-0.0284	0.0424	0.1449	0.0776	-0.0886	-0.1496	0.0562	-0.0229	0.3437	0.011	0.0853	0.2442	0.0095	0.0548	55.5113	9.6879	112.4649
22	11.7794	-10.0519	-1.0596	11.5589	3.873	4.6738	-0.1151	0.0171	-0.3428	0.2659	-0.1695	0.3251	0.1339	-0.322	0.2846	0.4434	0.0199	0.0734	0.4521	0.0053	0.1961	35.6406	17.1495	122.1648
23	9.9019	0.2036	-2.0843	0.9751	-0.2833	0.5205	0.0405	-0.497	-0.4667	0.1492	0.0261	0.6292	-0.0458	-0.0257	-0.0666	0.6028	0.016	0.0636	0.658	0.0191	0.4461	32.5789	35.0934	122.9568
24	3.2132	-0.9857	0.5187	3.1896	-0.8875	2.4435	-0.1527	0.0498	0.1461	0.1982	0.0486	-0.0499	-0.1679	0.0986	0.104	0.3939	-0.0204	0.013	0.3285	-0.0735	0.1334	56.7292	41.8483	120.884
25	1.712	0.4954	0.8953	1.6254	-0.3063	1.7761	-0.0622	0.0262	0.2717	-0.0005	-0.019	-0.1053	-0.1182	0.0592	0.0813	0.3919	-0.0084	0.0605	0.2606	-0.015	0.0929	53.5102	38.7088	111.6042
26	2.8488	1.55	0.7529	2.5435	-0.2313	0.9817	0.0187	0.027	0.2031	0.2051	0.0141	0.2455	-0.2271	-0.1364	-0.0328	0.3745	0.05	0.0625	0.2699	-0.0602	0.0542	41.2298	27.6517	104.5553
27	2.4916	-0.4489	-0.0535	2.4263	-0.4053	1.5867	0.0095	0.1579	0.1426	-0.2786	-0.0387	0.188	-0.0065	-0.0156	0.0291	0.3639	-0.0167	0.0331	0.2547	-0.0315	0.0471	45.8521	27.7275	102.0391
28	9.1369	1.5332	-3.1043	4.7656	-1.1482	4.2343	0.0145	-0.2375	-0.0431	-0.0261	-0.1125	-0.1371	0.1617	0.3468	0.098	0.31	0.0184	0.0167	0.2602	-0.0459	0.0221	58.8882	23.1543	116.1397

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 72
3	X-RAY DIFFRACTION	3	A	73 - 141
4	X-RAY DIFFRACTION	4	A	142 - 212
5	X-RAY DIFFRACTION	5	A	213 - 234
6	X-RAY DIFFRACTION	6	A	235 - 270
7	X-RAY DIFFRACTION	7	A	271 - 306
8	X-RAY DIFFRACTION	8	B	1 - 7
9	X-RAY DIFFRACTION	9	B	8 - 20
10	X-RAY DIFFRACTION	10	B	21 - 72
11	X-RAY DIFFRACTION	11	B	73 - 141
12	X-RAY DIFFRACTION	12	B	142 - 210
13	X-RAY DIFFRACTION	13	B	211 - 235
14	X-RAY DIFFRACTION	14	B	236 - 305
15	X-RAY DIFFRACTION	15	C	1 - 25
16	X-RAY DIFFRACTION	16	C	26 - 41
17	X-RAY DIFFRACTION	17	C	42 - 72
18	X-RAY DIFFRACTION	18	C	73 - 140
19	X-RAY DIFFRACTION	19	C	141 - 209
20	X-RAY DIFFRACTION	20	C	210 - 236
21	X-RAY DIFFRACTION	21	C	237 - 306
22	X-RAY DIFFRACTION	22	D	1 - 17
23	X-RAY DIFFRACTION	23	D	18 - 41
24	X-RAY DIFFRACTION	24	D	42 - 72
25	X-RAY DIFFRACTION	25	D	73 - 170
26	X-RAY DIFFRACTION	26	D	171 - 212
27	X-RAY DIFFRACTION	27	D	213 - 285
28	X-RAY DIFFRACTION	28	D	286 - 306

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