PDB-5wiz: Phosphotriesterase variant S5

ID or keywords:

Entry

Database: PDB / ID: 5wiz

Title

Phosphotriesterase variant S5

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: 1.96 Å

Authors

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

Citation

Journal: To Be Published
Title: Phosphotriesterase variant S5
Authors: Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.

History

Deposition	Jul 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 2019	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5wiz.cif.gz	248.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5wiz.ent.gz	208.4 KB	Display	PDB format
PDBx/mmJSON format	5wiz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5wiz_validation.pdf.gz	471.7 KB	Display	wwPDB validaton report
Full document	5wiz_full_validation.pdf.gz	478.5 KB	Display
Data in XML	5wiz_validation.xml.gz	24.7 KB	Display
Data in CIF	5wiz_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wi/5wiz ftp://data.pdbj.org/pub/pdb/validation_reports/wi/5wiz	HTTPS FTP

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Related structure data

Similar structure data	5wcr-d 5wj0-d 1p6b-d 4zst-d 4zsu-d 4re0-1 5vri-2 6aml-d 5w3z-1 5wms-2 6bhk-1 4xd4-d 4pbf-d 3urb-d 5w7h-d 5vsa-1 3ur5-d 5wcw-d 2oql-d 6fwe-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

72.6 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)	85.248, 85.688, 88.484
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: 35845.840 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: A0A060GYS1
#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.: 144 / 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: 2.25 Å³/Da / Density % sol: 45.43 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM NaCacodylate, 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: Oct 22, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.96→28.95 Å / Num. obs: 47044 / % possible obs: 99.7 % / Redundancy: 3.5 % / Net I/σ(I): 9.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→28.949 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.48

	R_factor	Num. reflection	% reflection
R_free	0.2329	2436	5.19 %
R_work	0.2116	-	-
obs	0.2128	46898	99.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.96→28.949 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4744	0	38	144	4926

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4923
X-RAY DIFFRACTION	f_angle_d	0.888	6704
X-RAY DIFFRACTION	f_dihedral_angle_d	12.909	1791
X-RAY DIFFRACTION	f_chiral_restr	0.031	792
X-RAY DIFFRACTION	f_plane_restr	0.004	859

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 (%)
1.96-2	0.3683	144	0.349	2582	X-RAY DIFFRACTION	100
2-2.0435	0.332	163	0.3367	2585	X-RAY DIFFRACTION	100
2.0435-2.091	0.3741	143	0.317	2574	X-RAY DIFFRACTION	100
2.091-2.1433	0.2941	127	0.2827	2612	X-RAY DIFFRACTION	100
2.1433-2.2012	0.2719	162	0.2553	2578	X-RAY DIFFRACTION	100
2.2012-2.266	0.2767	126	0.2559	2596	X-RAY DIFFRACTION	99
2.266-2.3391	0.2746	113	0.2446	2621	X-RAY DIFFRACTION	100
2.3391-2.4226	0.2725	164	0.2255	2584	X-RAY DIFFRACTION	100
2.4226-2.5196	0.2262	163	0.2281	2602	X-RAY DIFFRACTION	100
2.5196-2.6342	0.2571	116	0.2306	2612	X-RAY DIFFRACTION	100
2.6342-2.7729	0.2718	141	0.2252	2627	X-RAY DIFFRACTION	100
2.7729-2.9465	0.2472	164	0.223	2604	X-RAY DIFFRACTION	100
2.9465-3.1738	0.2525	140	0.2144	2640	X-RAY DIFFRACTION	100
3.1738-3.4927	0.2315	137	0.2029	2610	X-RAY DIFFRACTION	99
3.4927-3.9969	0.1987	128	0.1702	2676	X-RAY DIFFRACTION	99
3.9969-5.0314	0.1794	168	0.1577	2667	X-RAY DIFFRACTION	100
5.0314-28.9519	0.1701	137	0.1739	2692	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	1.1368	-0.0372	-0.2905	0.5223	0.1744	1.2202	0.0163	-0.0461	0.1495	-0.0026	0.043	-0.0511	-0.1894	0.1263	-0.0178	0.1706	-0.0122	0.0024	0.1189	0.0058	0.2115	23.6889	28.1481	36.5354
2	0.9989	0.6419	0.2578	1.3553	0.0188	1.5295	-0.079	-0.0784	-0.0735	0.0138	0.0213	0.0887	0.0991	-0.0833	0.036	0.1732	0.0303	0.0053	0.1385	0.0262	0.2078	15.4516	10.6165	36.1741
3	1.4586	0.8714	-0.6546	1.3042	0.7948	1.6342	0.1081	-0.3313	0.1512	0.0587	-0.0892	0.1531	0.0161	-0.2759	-0.0142	0.2711	-0.0081	0.0383	0.3779	0.0029	0.2686	9.3313	20.4994	53.3812
4	0.3912	-0.2432	-0.072	0.8416	0.2432	1.0489	0.1047	0.0157	0.2548	-0.0965	0.0023	0.1854	-0.3819	-0.3801	-0.1233	0.2914	0.0352	0.0392	0.2398	-0.0126	0.3475	12.5242	35.4297	39.7011
5	2.4131	-0.3127	-0.3488	1.4797	-0.2193	1.8274	-0.0313	-0.5497	0.0552	0.3613	-0.0747	0.1414	-0.1085	0.2573	0.1058	0.3378	-0.0609	-0.0095	0.3096	-0.0147	0.2621	19.2584	25.6169	57.6205
6	1.164	0.0693	0.0351	0.0886	0.5028	1.5708	-0.1155	0.5543	0.1795	-0.196	0.0813	0.0589	-0.2816	-0.18	0.0269	0.2625	0.0274	0.0106	0.5434	0.0428	0.2388	22.8085	24.3158	-2.9955
7	1.2867	-0.9409	0.1013	0.7336	0.3887	0.8271	-0.1235	0.3498	-0.1076	0.1749	0.0513	-0.1251	-0.0389	0.2418	0.0535	0.2411	0.0125	0.0107	0.1375	0.0002	0.2061	23.3185	12.4839	19.9749
8	0.892	-0.0684	-0.4202	0.7821	-0.1855	3.3125	-0.0211	0.5492	-0.2298	-0.248	-0.1307	-0.0106	0.3882	0.2907	0.0306	0.2702	0.0707	0.0292	0.4288	-0.0568	0.3069	29.8201	10.0501	4.7821
9	1.3708	-0.3172	0.3959	0.6801	0.2848	1.3099	-0.0855	0.1885	0.113	-0.0463	0.033	0.0339	-0.159	-0.0653	0.0326	0.2109	0.0281	-0.0133	0.2991	0.0552	0.1768	14.4657	26.274	10.0157
10	1.974	-0.1928	0.4705	0.4035	0.5161	1.0551	0.0198	0.4526	-0.1275	-0.1215	0.0562	0.1493	0.0997	-0.1896	-0.041	0.3001	0.0084	-0.0213	0.6003	0.0386	0.2411	2.1853	19.9265	-1.1088
11	0.9964	0.1095	0.461	0.7403	-0.5116	2.0763	0.0206	0.5667	-0.1946	-0.1499	0.0371	0.0152	0.1723	-0.0629	-0.0484	0.3211	0.0196	0.0046	0.6057	-0.0914	0.283	13.0394	11.4845	-5.898

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 36 through 135 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 136 through 219 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 220 through 298 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 299 through 330 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 331 through 362 )
6	X-RAY DIFFRACTION	6	chain 'G' and (resid 34 through 58 )
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 59 through 75 )
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 76 through 92 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 93 through 194 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 195 through 276 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 277 through 362 )

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