PDB-5wms: Phosphotriesterase variant S7

ID or keywords:

Entry

Database: PDB / ID: 5wms

Title

Phosphotriesterase variant S7

Components

Phosphotriesterase

Keywords

HYDROLASE / phosphotriesterase / organophosphate hydrolase / epistasis / directed evolution / laboratory evolution

Function / homology

Function and homology information

catabolic process / hydrolase activity, acting on ester bonds / zinc ion binding
Similarity search - Function

Biological species

Brevundimonas diminuta (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.

Citation

Journal: To Be Published
Title: Phosphotriesterase variant S7
Authors: Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.

History

Deposition	Jul 31, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5wms.cif.gz	490.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5wms.ent.gz	404.6 KB	Display	PDB format
PDBx/mmJSON format	5wms.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wms_validation.pdf.gz	508.3 KB	Display	wwPDB validaton report
Full document	5wms_full_validation.pdf.gz	526 KB	Display
Data in XML	5wms_validation.xml.gz	51.5 KB	Display
Data in CIF	5wms_validation.cif.gz	71.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wm/5wms ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wms	HTTPS FTP

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Related structure data

Related structure data	5wcpC 4cpcS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ura-d 5wcw-d 4keu-2 3c86-2 3ur2-d 4xd6-d 2r1k-2 6for-1 2r1m-2 4xaz-d 2ob3-d 4xay-d 3urq-d 4keu-1 2o4q-2 6bhl-d 6fu6-d 5wcr-d 4ket-1 6bh7-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

Related structure data

5wcpC

4cpcS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Phosphotriesterase

G: Phosphotriesterase

Q: Phosphotriesterase

S: Phosphotriesterase

hetero molecules

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

1

A: Phosphotriesterase

G: Phosphotriesterase

hetero molecules

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

2

Q: Phosphotriesterase

S: Phosphotriesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.658, 86.125, 176.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Phosphotriesterase Mass: 35729.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A060GYS1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.28 Å³/Da / Density % sol: 46.11 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM NaCacodylate, 10% 2-methane-2,4-pentanediol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.5→43.062 Å / Num. obs: 208968 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 17

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4CPC

4cpc

Resolution: 1.6→43.062 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2925	8643	5.02 %
R_work	0.2636	-	-
obs	0.265	172184	99.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→43.062 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9572	0	100	466	10138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	10048
X-RAY DIFFRACTION	f_angle_d	0.889	13627
X-RAY DIFFRACTION	f_dihedral_angle_d	14.699	5994
X-RAY DIFFRACTION	f_chiral_restr	0.052	1596
X-RAY DIFFRACTION	f_plane_restr	0.005	1749

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 (%)
1.6-1.6182	0.3414	286	0.3206	5374	X-RAY DIFFRACTION	100
1.6182-1.6372	0.3635	271	0.3176	5404	X-RAY DIFFRACTION	100
1.6372-1.6572	0.3598	290	0.3191	5388	X-RAY DIFFRACTION	100
1.6572-1.6782	0.3615	243	0.3023	5435	X-RAY DIFFRACTION	100
1.6782-1.7002	0.3224	286	0.3027	5383	X-RAY DIFFRACTION	100
1.7002-1.7235	0.316	296	0.2973	5428	X-RAY DIFFRACTION	100
1.7235-1.7482	0.3344	281	0.2882	5410	X-RAY DIFFRACTION	100
1.7482-1.7743	0.307	326	0.2948	5343	X-RAY DIFFRACTION	100
1.7743-1.802	0.3538	294	0.3032	5424	X-RAY DIFFRACTION	100
1.802-1.8315	0.3492	305	0.3014	5369	X-RAY DIFFRACTION	100
1.8315-1.8631	0.3243	342	0.2885	5362	X-RAY DIFFRACTION	100
1.8631-1.897	0.3248	269	0.286	5432	X-RAY DIFFRACTION	100
1.897-1.9335	0.302	318	0.291	5378	X-RAY DIFFRACTION	100
1.9335-1.9729	0.331	305	0.2844	5388	X-RAY DIFFRACTION	100
1.9729-2.0158	0.3003	287	0.2879	5443	X-RAY DIFFRACTION	100
2.0158-2.0627	0.3534	266	0.2829	5455	X-RAY DIFFRACTION	100
2.0627-2.1143	0.3006	296	0.2825	5409	X-RAY DIFFRACTION	100
2.1143-2.1715	0.3145	293	0.2823	5418	X-RAY DIFFRACTION	100
2.1715-2.2354	0.3054	300	0.2737	5450	X-RAY DIFFRACTION	100
2.2354-2.3075	0.324	246	0.2747	5503	X-RAY DIFFRACTION	100
2.3075-2.39	0.2853	277	0.2791	5454	X-RAY DIFFRACTION	100
2.39-2.4857	0.3087	290	0.2716	5460	X-RAY DIFFRACTION	100
2.4857-2.5988	0.3228	297	0.2721	5488	X-RAY DIFFRACTION	100
2.5988-2.7358	0.2847	295	0.2684	5438	X-RAY DIFFRACTION	100
2.7358-2.9071	0.2668	282	0.2573	5503	X-RAY DIFFRACTION	100
2.9071-3.1315	0.2955	280	0.2598	5517	X-RAY DIFFRACTION	100
3.1315-3.4466	0.2976	291	0.2481	5549	X-RAY DIFFRACTION	100
3.4466-3.945	0.2381	279	0.2367	5568	X-RAY DIFFRACTION	100
3.945-4.9691	0.2494	276	0.227	5614	X-RAY DIFFRACTION	100
4.9691-43.0781	0.2541	276	0.234	5754	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	1.7976	0.2504	-0.3506	2.3668	-0.1604	4.8991	0.0145	0.2196	0.1558	-0.2541	-0.1612	-0.5321	-0.0659	0.6184	0.1437	0.2077	0.0303	0.0384	0.3905	0.0268	0.3344	33.7682	21.9131	43.503
2	0.1695	-0.1384	-0.1079	0.2726	0.0375	0.5389	0.0116	0.0105	0.016	-0.0249	-0.0048	-0.0177	0.082	0.0397	0.0073	0.1327	0.0554	0.0321	-0.0291	-0.1302	0.1552	21.4734	9.2247	54.4524
3	0.706	-0.6352	-0.5603	1.7638	0.5922	1.2109	-0.0744	-0.1579	0.2685	0.0911	0.0193	-0.0494	-0.0951	-0.026	-0.0416	0.1494	0.0971	0.005	0.1	-0.1841	0.3043	21.4278	24.4414	54.6414
4	0.7102	-0.0479	-0.2245	1.4281	0.0969	1.2946	-0.0456	-0.045	0.4377	-0.049	-0.0335	0.2066	0.0214	-0.2471	0.0676	0.2495	-0.0509	0.0179	0.7251	0.0217	0.4182	11.2145	31.9462	45.1302
5	0.2417	-0.572	0.3794	1.7003	-0.4505	1.1812	0.0422	0.283	0.1677	-0.4038	-0.035	0.2165	0.0304	-0.0748	-0.002	0.2708	0.079	-0.0039	0.5787	0.134	0.263	8.8883	20.2049	34.0331
6	0.2162	0.1648	0.1572	0.9816	0.3056	0.8363	0.0166	-0.0274	-0.0349	0.0684	-0.0689	0.1039	0.1186	-0.1031	0.0439	0.1384	-0.0348	0.0157	-0.044	-0.079	0.148	12.4383	7.2227	49.04
7	1.2916	0.0181	0.4316	1.9597	0.3966	2.3952	-0.0377	0.1509	0.0814	-0.4086	-0.0042	-0.117	-0.1081	0.1625	0.0138	0.1644	0.058	0.0486	0.0592	0.1415	0.1867	19.7038	18.0382	31.0422
8	0.0611	0.0006	0.0939	0.2075	0.2692	1.2693	-0.033	-0.1371	0.0926	0.0718	-0.0165	-0.0446	-0.0983	0.0265	-0.0789	0.1745	-0.048	-0.036	0.4796	-0.4858	0.2519	24.0199	25.2144	82.5808
9	0.1231	0.1043	0.0947	0.3812	0.3013	0.6487	-0.0241	-0.1005	0.0643	0.0096	0.0313	-0.0383	0.038	0.0137	0.017	0.1324	-0.0002	0.0257	0.2808	-0.3655	0.097	13.8521	14.9361	77.6292
10	0.0422	0.0394	-0.0715	0.0604	0.0769	0.4363	0.0178	-0.1276	0.1467	-0.018	0.0056	-0.0075	-0.2074	-0.0227	-0.0195	0.2481	0.056	0.0448	0.6663	-0.6127	0.2079	7.4746	28.4335	89.9714
11	0.8448	-1.0029	-0.3861	2.3541	0.7937	3.2614	0.001	-0.034	0.0362	0.2475	-0.0401	0.0642	-0.0709	0.0105	0.031	0.2069	-0.0302	0.0138	0.5044	-0.3053	0.3078	14.2781	24.8028	101.0634
12	1.7428	1.4616	-0.8842	1.6015	0.4416	4.1838	0.0348	-0.0992	0.0346	0.1014	0.1142	-0.152	0.0368	0.1355	-0.1484	0.1837	0.0271	-0.0081	0.2121	0.0446	0.364	-14.1358	22.9624	45.4192
13	0.5496	-0.0504	0.5923	0.083	0.0983	0.979	0.0241	0.1761	0.4018	-0.0845	-0.0534	-0.1094	-0.1517	0.062	0.1065	0.2796	0.0744	0.0269	0.6559	0.2914	0.4963	-20.9299	32.3419	33.541
14	1.5872	0.7342	0.7582	2.0165	1.1587	1.971	0.0771	0.0326	0.089	-0.0541	0.1441	-0.2366	-0.0683	-0.0069	-0.1914	0.2072	0.0613	0.0308	0.3576	0.1569	0.3506	-18.8556	25.3828	35.2002
15	1.3579	0.3493	1.5651	1.5216	-0.3434	2.7664	0.0671	0.0666	-0.0239	-0.0948	0.0021	-0.0145	0.1592	0.0426	-0.0537	0.174	0.0789	0.011	0.2863	0.1516	0.1881	-23.9013	8.8825	28.444
16	0.8832	0.835	0.0427	1.5413	-0.149	1.3133	-0.0056	-0.0312	0.1043	0.0188	-0.0114	-0.0119	-0.0029	0.0749	0.0145	0.1764	0.1096	0.0007	0.2568	0.106	0.2283	-23.0956	15.6743	34.7703
17	0.1527	0.1796	-0.0014	0.2938	-0.0471	0.7003	-0.0157	-0.0763	0.2445	0.1086	0.0014	0.1556	-0.2153	-0.1313	0.0171	0.1273	0.0327	0.0126	-0.1754	0.0118	0.2545	-32.6085	14.1025	45.6841
18	0.7933	0.4148	-0.598	1.4482	0.4499	1.8588	0.0812	-0.1103	0.2451	0.1245	-0.0351	0.2417	-0.1726	-0.1392	-0.0353	0.3058	0.015	0.0792	0.2474	-0.1999	0.3732	-32.9796	24.5061	57.9629
19	0.4136	0.0515	0.2652	0.3829	0.4186	1.4027	0.0044	-0.0654	0.2907	-0.0361	0.0328	0.1297	-0.1715	-0.1877	-0.0331	0.3718	0.0494	0.1201	0.6354	0.1509	0.7025	-30.4013	35.7265	39.3926
20	1.9404	-0.5158	-0.1505	1.6285	-0.128	2.5382	-0.0431	-0.2793	0.2962	0.4944	0.0535	0.178	-0.1066	0.0615	-0.0209	0.3449	-0.0123	0.0431	0.6104	-0.2469	0.3907	-22.944	24.5958	57.333
21	0.2479	-0.0037	0.0116	0.1561	0.0214	0.9313	0.0107	0.1735	0.1662	-0.0706	0.0197	-0.0094	-0.1111	-0.0076	0.0071	0.2311	-0.0138	0.0258	0.4133	0.3948	0.295	-19.5012	19.8339	7.2245
22	0.4912	0.0361	0.0605	0.4479	0.4285	4.3064	-0.0046	0.1761	0.043	-0.1301	-0.0159	-0.0533	0.1795	0.0884	0.0266	0.2255	0.0214	0.0383	0.4276	0.2432	0.3201	-12.661	10.3988	4.7652
23	0.064	0.0093	-0.041	0.0029	-0.0186	0.0232	-0.0315	0.0464	0.1057	-0.0083	-0.0254	0.006	-0.0364	-0.001	-0.1238	0.2317	0.0098	-0.0142	0.6953	0.8031	0.2559	-28.0705	26.5721	10.0055
24	0.09	-0.0267	-0.0265	0.1461	-0.1971	0.7299	-0.0088	0.055	-0.0292	-0.0395	0.0064	0.0205	0.1534	-0.0341	-0.0444	0.255	-0.0064	-0.0416	0.6959	0.593	0.341	-39.4671	18.0783	-3.7588
25	0.1266	-0.1486	-0.0206	0.6727	-0.4555	2.1199	0.0175	0.1257	0.046	-0.0892	-0.0259	0.0116	0.2517	-0.0459	0.0192	0.2252	-0.0852	-0.0203	0.4642	0.3848	0.2508	-26.6999	11.8244	-3.8609

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 34 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 92 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 93 through 177 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 178 through 236 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 237 through 298 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 299 through 330 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 331 through 363 )
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 33 through 109 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 110 through 194 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 195 through 330 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 331 through 363 )
12	X-RAY DIFFRACTION	12	chain 'Q' and (resid 33 through 58 )
13	X-RAY DIFFRACTION	13	chain 'Q' and (resid 59 through 109 )
14	X-RAY DIFFRACTION	14	chain 'Q' and (resid 110 through 135 )
15	X-RAY DIFFRACTION	15	chain 'Q' and (resid 136 through 155 )
16	X-RAY DIFFRACTION	16	chain 'Q' and (resid 156 through 177 )
17	X-RAY DIFFRACTION	17	chain 'Q' and (resid 178 through 276 )
18	X-RAY DIFFRACTION	18	chain 'Q' and (resid 277 through 298 )
19	X-RAY DIFFRACTION	19	chain 'Q' and (resid 299 through 330 )
20	X-RAY DIFFRACTION	20	chain 'Q' and (resid 331 through 363 )
21	X-RAY DIFFRACTION	21	chain 'S' and (resid 34 through 75 )
22	X-RAY DIFFRACTION	22	chain 'S' and (resid 76 through 92 )
23	X-RAY DIFFRACTION	23	chain 'S' and (resid 93 through 194 )
24	X-RAY DIFFRACTION	24	chain 'S' and (resid 195 through 298 )
25	X-RAY DIFFRACTION	25	chain 'S' and (resid 299 through 363 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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