PDB-4le6: Crystal structure of the phosphotriesterase OPHC2 from Pseudomona...

ID or keywords:

Entry

Database: PDB / ID: 4le6

Title

Crystal structure of the phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes

Components

Organophosphorus hydrolase

Keywords

HYDROLASE / alpha beta/beta alpha sandwich / metallo-hydrolase / phosphotriesterase

Function / homology

Function and homology information

aryldialkylphosphatase activity / aryldialkylphosphatase / metal ion binding
Similarity search - Function

Biological species

Pseudomonas pseudoalcaligenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Gotthard, G. / Hiblot, J. / Chabriere, E. / Elias, M.

Citation

Journal: Plos One / Year: 2013
Title: Structural and Enzymatic Characterization of the Phosphotriesterase OPHC2 from Pseudomonas pseudoalcaligenes.
Authors: Gotthard, G. / Hiblot, J. / Gonzalez, D. / Elias, M. / Chabriere, E.

History

Deposition	Jun 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2013	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4le6.cif.gz	724.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4le6.ent.gz	613.6 KB	Display	PDB format
PDBx/mmJSON format	4le6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4le6_validation.pdf.gz	511.4 KB	Display	wwPDB validaton report
Full document	4le6_full_validation.pdf.gz	536.9 KB	Display
Data in XML	4le6_validation.xml.gz	53.4 KB	Display
Data in CIF	4le6_validation.cif.gz	74.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/le/4le6 ftp://data.pdbj.org/pub/pdb/validation_reports/le/4le6	HTTPS FTP

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Related structure data

Related structure data	1p9eS S: Starting model for refinement
Similar structure data	3kfc-2 6deu-2 5m6b-4 3ozv-2 1g0n-d 3qfd-2 7c1p-3 6m8q-1 2gvi-1 6k8p-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1p9eS

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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Organophosphorus hydrolase

B: Organophosphorus hydrolase

C: Organophosphorus hydrolase

D: Organophosphorus hydrolase

E: Organophosphorus hydrolase

hetero molecules

177 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Organophosphorus hydrolase

hetero molecules

A: Organophosphorus hydrolase

hetero molecules

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

2

B: Organophosphorus hydrolase

C: Organophosphorus hydrolase

hetero molecules

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

3

D: Organophosphorus hydrolase

E: Organophosphorus hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.910, 63.850, 221.260
Angle α, β, γ (deg.)	90.00, 101.85, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-751- HOH
2	1	A-771- HOH
3	1	A-795- HOH

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	Organophosphorus hydrolase Mass: 34959.738 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas pseudoalcaligenes (bacteria) Gene: ophc2 / Plasmid: pET22-b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pGro7/GroEL / References: UniProt: Q5W503, aryldialkylphosphatase

#1: Protein

Organophosphorus hydrolase

Mass: 34959.738 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas pseudoalcaligenes (bacteria)
Gene: ophc2 / Plasmid: pET22-b(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pGro7/GroEL / References: UniProt: Q5W503, aryldialkylphosphatase

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Non-polymers , 5 types, 705 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.17 Å³/Da / Density % sol: 43.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEG 8000, 100 mM Tris buffer, 200 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 2.1→42.8 Å / Num. obs: 82520

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: dev_1352)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1P9E

1p9e

Resolution: 2.1→42.8 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 20.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2099	4126	5 %
R_work	0.1733	-	-
obs	0.1751	82520	93.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→42.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9618	0	84	682	10384

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	9992
X-RAY DIFFRACTION	f_angle_d	0.988	13612
X-RAY DIFFRACTION	f_dihedral_angle_d	14.562	3567
X-RAY DIFFRACTION	f_chiral_restr	0.06	1528
X-RAY DIFFRACTION	f_plane_restr	0.005	1787

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 (%)
2.1-2.1247	0.2675	127	0.243	2411	X-RAY DIFFRACTION	81
2.1247-2.1506	0.2635	120	0.2288	2290	X-RAY DIFFRACTION	83
2.1506-2.1779	0.2482	126	0.2105	2393	X-RAY DIFFRACTION	83
2.1779-2.2065	0.2328	129	0.2113	2451	X-RAY DIFFRACTION	84
2.2065-2.2367	0.2392	129	0.2014	2436	X-RAY DIFFRACTION	86
2.2367-2.2687	0.2523	134	0.196	2544	X-RAY DIFFRACTION	87
2.2687-2.3026	0.2411	130	0.194	2475	X-RAY DIFFRACTION	88
2.3026-2.3385	0.2034	135	0.1825	2560	X-RAY DIFFRACTION	89
2.3385-2.3769	0.2423	133	0.1855	2541	X-RAY DIFFRACTION	89
2.3769-2.4179	0.2506	138	0.1856	2616	X-RAY DIFFRACTION	92
2.4179-2.4618	0.2271	139	0.1772	2649	X-RAY DIFFRACTION	92
2.4618-2.5092	0.2082	143	0.1865	2715	X-RAY DIFFRACTION	95
2.5092-2.5604	0.2358	144	0.1858	2732	X-RAY DIFFRACTION	94
2.5604-2.616	0.2226	146	0.1834	2778	X-RAY DIFFRACTION	97
2.616-2.6769	0.2127	147	0.174	2778	X-RAY DIFFRACTION	97
2.6769-2.7438	0.2233	147	0.1736	2793	X-RAY DIFFRACTION	97
2.7438-2.818	0.2129	146	0.1758	2776	X-RAY DIFFRACTION	98
2.818-2.9009	0.2233	154	0.1795	2927	X-RAY DIFFRACTION	99
2.9009-2.9945	0.2255	146	0.1688	2784	X-RAY DIFFRACTION	99
2.9945-3.1015	0.2073	148	0.1754	2816	X-RAY DIFFRACTION	99
3.1015-3.2256	0.2231	151	0.1809	2863	X-RAY DIFFRACTION	99
3.2256-3.3724	0.1852	152	0.1697	2883	X-RAY DIFFRACTION	99
3.3724-3.5501	0.2105	150	0.1618	2859	X-RAY DIFFRACTION	99
3.5501-3.7724	0.2033	150	0.162	2846	X-RAY DIFFRACTION	99
3.7724-4.0635	0.1984	149	0.1594	2831	X-RAY DIFFRACTION	98
4.0635-4.472	0.2014	151	0.1446	2858	X-RAY DIFFRACTION	98
4.472-5.1182	0.1719	151	0.1484	2884	X-RAY DIFFRACTION	99
5.1182-6.4449	0.1977	155	0.1725	2934	X-RAY DIFFRACTION	99
6.4449-42.8093	0.2073	156	0.1926	2972	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	1.5989	-0.2727	-0.1991	0.5636	-0.2061	0.8533	0.0282	0.194	-0.0848	-0.0732	-0.0362	0.0401	-0.0174	0.0137	0.001	0.1679	0.0061	-0.0473	0.1045	-0.015	0.2584	9.9427	-17.9219	-6.9149
2	4.257	-1.2095	1.2199	5.4594	-2.5417	6.7631	-0.0302	-0.0208	-0.2066	-0.0744	-0.0148	-0.5045	0.2151	0.5347	0.0179	0.1281	-0.02	-0.0057	0.1796	-0.0387	0.3879	26.1938	-11.5114	-2.602
3	1.4506	-0.0752	-0.1984	1.311	0.292	0.8122	0.0341	0.0239	-0.4023	-0.0089	0.0006	-0.0888	0.163	0.1168	-0.0176	0.2148	0.0136	-0.0866	0.145	-0.0073	0.3759	14.5224	-29.8516	-0.6659
4	3.0184	-0.2434	-0.9027	1.0608	0.1232	1.9798	0.0838	0.1559	0.1468	-0.0486	-0.0561	0.1252	-0.0349	0.0354	-0.0479	0.2113	0.0852	0.0046	0.2205	0.0266	0.2234	28.434	-18.6287	-31.2147
5	1.5997	0.7741	-1.6237	4.3911	-3.5242	7.6373	0.5646	-0.0805	0.8681	0.1456	0.2128	0.4419	-0.8584	-0.666	-0.6681	0.4653	-0.0278	0.2392	0.3659	-0.0095	0.6264	26.3871	-2.4768	-24.3463
6	1.538	-0.4277	-0.1761	2.16	-0.2991	1.9503	0.3398	0.7535	0.2751	-0.3165	-0.1513	0.365	-0.1858	-0.383	-0.1616	0.3667	0.1821	-0.0288	0.49	0.0456	0.3744	18.7443	-15.3558	-41.0458
7	1.156	0.6454	-0.5519	1.2838	0.6982	1.3429	0.0733	0.4657	0.0215	-0.2704	-0.1959	-0.2093	0.0197	0.1021	0.1068	0.4037	0.2491	0.0531	0.5857	0.0634	0.2951	43.8774	-26.2678	-48.3922
8	2.6065	0.3724	-0.1793	0.5747	-0.1693	1.3	-0.029	0.5483	-0.6584	-0.1861	-0.0441	-0.1559	0.5222	0.3233	0.1048	0.501	0.2613	0.076	0.6282	-0.0784	0.4749	48.7563	-40.3796	-48.7163
9	2.2956	-0.2929	-1.1778	2.6412	0.3844	1.9809	-0.032	0.8241	-0.486	-0.5549	-0.1629	0.1996	0.3483	-0.1181	0.2306	0.4715	0.2019	-0.0364	0.664	-0.1401	0.4111	32.9129	-34.8246	-52.2274
10	2.2412	-0.3089	-0.106	2.5252	0.2251	2.4156	0.2485	0.431	0.3075	-0.4255	0.0042	-0.2624	-0.4671	-0.2629	-0.2017	0.7234	0.1966	0.19	0.897	0.0593	0.3925	6.5437	5.0852	-73.031
11	1.1642	-1.0689	0.4033	1.9982	0.5462	1.0242	0.2181	-0.1618	0.5531	-0.2434	0.1616	-0.7455	-0.6259	0.5221	-0.3679	0.9044	0.0689	0.2954	0.9998	-0.0606	0.7888	14.1552	13.3224	-63.8318
12	0.1009	0.1916	-0.445	0.4211	-1.0644	2.8064	0.3275	0.3973	0.5763	-0.4096	-0.1702	-0.1067	-0.1411	0.0215	-0.1946	1.2241	0.5083	0.4242	1.1758	0.2627	0.8122	-3.1782	18.9322	-73.1636
13	1.6373	0.0348	-0.5776	0.5415	1.3529	3.6508	0.4925	0.4082	0.8826	-0.9472	-0.1143	-0.4768	-1.3248	-0.0881	-0.5871	1.4025	0.279	0.5464	0.941	0.2027	0.8328	8.9819	19.0879	-79.15
14	0.4022	0.0355	-0.7388	2.4311	-0.9471	1.6791	0.063	0.6163	0.5005	-0.9735	0.0347	-0.3826	-0.5284	-0.2535	-0.0662	1.237	0.145	0.412	1.2403	0.1281	0.6949	14.5125	5.6203	-92.3623
15	0.5059	0.3298	-0.4208	0.3243	-0.1648	0.7559	0.0031	0.5478	-0.053	-0.4272	-0.0815	-0.2105	0.2135	-0.2705	0.1871	1.5151	0.2222	0.5739	1.3718	-0.0441	0.6463	15.1525	-3.7214	-98.2552
16	0.5162	0.2153	-0.9635	0.8092	-0.2594	1.8268	-0.2541	0.1608	0.0096	-0.4566	0.6831	-0.0071	0.0833	-0.5367	-0.3891	1.5451	0.3842	0.129	2.2591	-0.0768	0.618	2.1834	-4.7758	-106.5194
17	0.1235	0.147	0.1213	0.2274	0.289	0.5133	-0.0872	0.4598	0.0991	-0.4463	0.1907	-0.0634	-0.3965	0.0525	-0.0654	1.9772	0.5893	0.4911	1.9267	0.3385	0.7768	5.8188	11.9879	-106.7924
18	0.585	-0.0576	-0.3058	0.7776	0.4988	0.5561	0.0533	0.5913	0.1923	-0.5568	-0.039	0.1233	-0.6558	-0.9131	-0.2799	1.1906	0.4331	0.2659	1.4221	0.1283	0.4548	1.0435	6.6279	-92.0622

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 25:148 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 149:217 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 218:324 )
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESID 25:148 )
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESID 149:217 )
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESID 218:324 )
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESID 26:148 )
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESID 149:246 )
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESID 247:324 )
10	X-RAY DIFFRACTION	10	CHAIN D AND (RESID 26:148 )
11	X-RAY DIFFRACTION	11	CHAIN D AND (RESID 149:246 )
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESID 247:268 )
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESID 269:323 )
14	X-RAY DIFFRACTION	14	CHAIN E AND (RESID 26:71 )
15	X-RAY DIFFRACTION	15	CHAIN E AND (RESID 72:158 )
16	X-RAY DIFFRACTION	16	CHAIN E AND (RESID 159:244 )
17	X-RAY DIFFRACTION	17	CHAIN E AND (RESID 245:286 )
18	X-RAY DIFFRACTION	18	CHAIN E AND (RESID 287:323 )

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 5 molecules ABCDE

-
Non-polymers , 5 types, 705 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi