PDB-5wcw: Phosphotriesterase variant S3

ID or keywords:

Entry

Database: PDB / ID: 5wcw

Title

Phosphotriesterase variant S3

Components

Phosphotriesterase

Keywords

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

Function / homology

Function and homology information

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

Biological species

Brevundimonas diminuta (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.457 Å

Authors

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

Citation

Journal: To Be Published
Title: Phosphotriesterase variant S4
Authors: Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.

History

Deposition	Jul 2, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2023	Group: Database references / Derived calculations / Structure summary Category: database_2 / entity ...database_2 / entity / struct / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	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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PDBx/mmCIF format	5wcw.cif.gz	265.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5wcw.ent.gz	213.5 KB	Display	PDB format
PDBx/mmJSON format	5wcw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wcw_validation.pdf.gz	476.8 KB	Display	wwPDB validaton report
Full document	5wcw_full_validation.pdf.gz	487.9 KB	Display
Data in XML	5wcw_validation.xml.gz	26.6 KB	Display
Data in CIF	5wcw_validation.cif.gz	37.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wc/5wcw ftp://data.pdbj.org/pub/pdb/validation_reports/wc/5wcw	HTTPS FTP

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Related structure data

Related structure data	4cpcS S: Starting model for refinement
Similar structure data	3urq-d 3ur2-d 3ura-d 5wms-1 5wcr-d 5wms-2 4zsu-d 4pbe-d 2r1m-2 3ur5-d 6gbl-d 6gbk-d 6aml-d 1psc-d 2ob3-d 4xd6-d 4xag-d 2o4q-2 4e3t-d 1eyw-1 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
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

hetero molecules

72.7 kDa, 2 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)	85.513, 85.887, 88.370
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: 35921.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A060GZX0
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.26 Å³/Da / Density % sol: 45.54 %
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: MX1 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 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: 1.457→38.62 Å / Num. obs: 113962 / % possible obs: 99.42 % / Redundancy: 7.5 % / Net I/σ(I): 13.76

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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: 1.457→39.254 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2343	5676	5.01 %
R_work	0.2083	-	-
obs	0.2096	113361	99.41 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.457→39.254 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4766	0	38	230	5034

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.025	4975
X-RAY DIFFRACTION	f_angle_d	0.978	6742
X-RAY DIFFRACTION	f_dihedral_angle_d	18.163	1804
X-RAY DIFFRACTION	f_chiral_restr	0.075	791
X-RAY DIFFRACTION	f_plane_restr	0.006	865

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 (%)
1.4569-1.4734	0.3391	163	0.3012	3298	X-RAY DIFFRACTION	92
1.4734-1.4908	0.332	202	0.2793	3532	X-RAY DIFFRACTION	100
1.4908-1.509	0.3076	197	0.2682	3576	X-RAY DIFFRACTION	100
1.509-1.5281	0.3101	190	0.2551	3564	X-RAY DIFFRACTION	100
1.5281-1.5482	0.2735	171	0.2467	3569	X-RAY DIFFRACTION	100
1.5482-1.5694	0.2707	192	0.2351	3555	X-RAY DIFFRACTION	100
1.5694-1.5918	0.2738	184	0.2408	3579	X-RAY DIFFRACTION	100
1.5918-1.6155	0.2877	180	0.2426	3605	X-RAY DIFFRACTION	100
1.6155-1.6408	0.2718	174	0.2442	3609	X-RAY DIFFRACTION	100
1.6408-1.6677	0.2909	210	0.2521	3544	X-RAY DIFFRACTION	100
1.6677-1.6965	0.3136	188	0.2565	3552	X-RAY DIFFRACTION	100
1.6965-1.7273	0.283	195	0.2536	3591	X-RAY DIFFRACTION	100
1.7273-1.7605	0.2834	193	0.2371	3575	X-RAY DIFFRACTION	100
1.7605-1.7965	0.2275	186	0.2297	3574	X-RAY DIFFRACTION	100
1.7965-1.8355	0.2531	184	0.2317	3611	X-RAY DIFFRACTION	100
1.8355-1.8782	0.2581	201	0.232	3559	X-RAY DIFFRACTION	100
1.8782-1.9252	0.3492	171	0.3054	3549	X-RAY DIFFRACTION	98
1.9252-1.9772	0.2782	153	0.2478	3557	X-RAY DIFFRACTION	99
1.9772-2.0354	0.2541	202	0.2175	3600	X-RAY DIFFRACTION	100
2.0354-2.1011	0.2356	193	0.2166	3595	X-RAY DIFFRACTION	100
2.1011-2.1762	0.2409	200	0.2157	3607	X-RAY DIFFRACTION	100
2.1762-2.2633	0.2817	182	0.2679	3541	X-RAY DIFFRACTION	98
2.2633-2.3663	0.2684	208	0.2195	3536	X-RAY DIFFRACTION	98
2.3663-2.4911	0.2262	186	0.2027	3612	X-RAY DIFFRACTION	100
2.4911-2.6471	0.2452	180	0.1966	3629	X-RAY DIFFRACTION	100
2.6471-2.8514	0.1986	192	0.192	3670	X-RAY DIFFRACTION	100
2.8514-3.1383	0.2269	203	0.1871	3627	X-RAY DIFFRACTION	100
3.1383-3.5921	0.1998	200	0.1826	3677	X-RAY DIFFRACTION	100
3.5921-4.5246	0.1835	182	0.1645	3732	X-RAY DIFFRACTION	100
4.5246-39.2687	0.1909	214	0.1772	3860	X-RAY DIFFRACTION	100

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	1.7182	0.1477	-0.069	0.4084	-0.1074	1.1806	-0.0179	0.0501	-0.1975	0.0568	-0.008	0.0451	0.1093	-0.0784	0.0281	0.173	-0.0033	0.0052	0.0921	-0.0089	0.2018	-24.0482	15.8402	-7.9488
2	1.5362	0.1087	-0.6161	0.6894	-0.5923	2.4949	-0.0152	0.0682	-0.5205	0.0797	-0.0038	0.0766	0.33	-0.1193	0.0242	0.2698	-0.0328	0.035	0.1072	-0.0098	0.331	-25.7297	4.5595	-6.2037
3	1.9168	0.1212	-0.3098	0.5274	-0.1335	1.3469	0.0007	0.1367	0.0006	0.0263	0.0241	0.0752	-0.0069	-0.0387	-0.0064	0.1405	0.008	-0.0017	0.0795	-0.0138	0.1523	-21.836	23.5377	-10.6966
4	2.3922	0.2632	-0.1201	0.7897	0.0593	1.4314	0.0201	0.0293	0.1427	0.0459	-0.0063	-0.0341	-0.0525	-0.0272	0.0048	0.1733	0.0238	-0.0009	0.0926	0.0079	0.1932	-19.869	27.3846	-9.5938
5	1.9389	0.0856	-0.0715	0.7097	-0.1179	1.4165	0.0344	-0.1956	0.0764	0.1478	-0.0321	-0.1099	-0.093	0.1673	-0.0126	0.1897	-0.0025	-0.015	0.122	-0.0269	0.2024	-10.2198	29.3761	1.5079
6	2.7581	-0.1295	0.2479	1.4415	-0.0994	1.9011	0.0438	-0.6777	-0.1953	0.325	0.0215	-0.1939	0.049	0.2485	-0.0025	0.3113	-0.0443	-0.049	0.3681	0.0698	0.225	-9.9528	18.4607	13.6923
7	1.1285	-0.0206	0.0486	0.4479	-0.0925	0.8426	0.0176	-0.0068	-0.491	0.0239	-0.0313	-0.1053	0.3437	0.2258	0.041	0.2567	0.0266	-0.0238	0.1521	0.0051	0.3294	-12.6094	7.2698	-4.9906
8	2.6631	-0.26	0.1072	1.3156	-0.1641	2.0754	0.0119	-0.6024	-0.1594	0.3771	-0.0402	-0.0383	0.0317	-0.0471	0.0094	0.2598	-0.0349	-0.0049	0.2703	0.0427	0.2044	-19.8923	18.417	13.0295
9	1.2064	0.1239	-0.0697	0.0307	-0.071	0.2263	0.0201	0.8544	-0.2799	-0.1829	0.006	-0.0475	0.0985	-0.0039	-0.0794	0.2695	-0.0036	-0.0318	1.012	-0.1612	0.307	-24.6055	15.8635	-48.7616
10	0.0155	0.0293	0.0601	0.1392	-0.0646	1.1595	0.021	0.8056	0.1222	-0.1199	-0.0318	0.0741	-0.1738	-0.1431	-0.0355	0.2028	0.0249	-0.0079	0.5293	0.0405	0.1875	-23.7539	28.7366	-34.5597
11	0.7947	0.0497	0.1946	0.411	-0.0172	1.1485	-0.0409	0.6288	-0.2272	-0.0504	-0.0067	-0.0165	0.1399	-0.024	-0.0384	0.1899	-0.0002	0.0252	0.4853	-0.1117	0.2125	-13.8402	15.2029	-33.1476
12	1.1216	-0.2718	-0.288	0.0727	-0.0073	0.9607	0.0322	0.5301	0.0511	-0.0539	-0.0301	-0.044	-0.0847	0.0842	-0.1626	0.2398	0.0089	0.0283	0.8915	-0.0777	0.214	-2.3331	22.4326	-45.3095
13	0.2985	-0.0346	-0.2401	0.098	-0.148	0.9616	0.081	0.6875	0.0927	-0.1334	-0.0524	-0.0436	-0.2323	-0.0086	-0.0729	0.3136	0.0211	0.0219	1.0324	0.1272	0.2278	-13.2664	30.7952	-49.9213

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 36 through 75 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 76 through 92 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 93 through 155 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 156 through 177 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 276 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 277 through 298 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 299 through 330 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 331 through 363 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 34 through 53 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 54 through 109 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 110 through 194 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 195 through 276 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 277 through 363 )

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