PDB-6aml: Phosphotriesterase variant S8

ID or keywords:

Entry

Database: PDB / ID: 6aml

Title

Phosphotriesterase variant S8

Components

Phosphotriesterase

Keywords

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

Function / homology

Function and homology information

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

Biological species

Brevundimonas diminuta (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.46 Å

Authors

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

Citation

Journal: To Be Published
Title: Phosphotriesterase variant S8
Authors: Miton, C.M. / Campbell, E.C. / Jackson, C.J. / Tokuriki, N.

History

Deposition	Aug 9, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2018	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_ptnr1_label_alt_id / _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	6aml.cif.gz	290.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6aml.ent.gz	235.5 KB	Display	PDB format
PDBx/mmJSON format	6aml.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6aml_validation.pdf.gz	475.7 KB	Display	wwPDB validaton report
Full document	6aml_full_validation.pdf.gz	484.4 KB	Display
Data in XML	6aml_validation.xml.gz	30.3 KB	Display
Data in CIF	6aml_validation.cif.gz	44.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/am/6aml ftp://data.pdbj.org/pub/pdb/validation_reports/am/6aml	HTTPS FTP

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Related structure data

Related structure data	4cpcS S: Starting model for refinement
Similar structure data	5w3z-1 4kev-2 5wcr-d 3ur5-d 5wcw-d 5wcq-d 5wiz-d 5vri-2 5wms-2 5w3w-1 4keu-2 2vc5-1 5w3w-2 3urq-d 5wj0-d 3fdk-1 3ur2-d 3urb-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
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2) #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)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#220 - Apr 2018
Dehalogenases
similarity (2)
#111 - Mar 2009
Hydrogenase
similarity (2)
#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)	85.134, 85.811, 88.658
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Phosphotriesterase / Phosphotriesterase variant PTE-R0 Mass: 35684.598 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, UniProt: P0A434*PLUS
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.27 Å³/Da / Density % sol: 45.82 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium cacodylate, 10% MPD

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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: May 2, 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: 1.46→42.57 Å / Num. obs: 112907 / % possible obs: 99.9 % / Redundancy: 13.5 % / Net I/σ(I): 20.4
Reflection shell	Highest resolution: 1.46 Å

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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: PDB entry 4CPC

4cpc

Resolution: 1.46→42.567 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1749	5532	4.9 %
R_work	0.153	-	-
obs	0.1541	112811	99.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.46→42.567 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4778	0	70	410	5258

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	5742
X-RAY DIFFRACTION	f_angle_d	1.56	7881
X-RAY DIFFRACTION	f_dihedral_angle_d	19.265	2149
X-RAY DIFFRACTION	f_chiral_restr	0.126	910
X-RAY DIFFRACTION	f_plane_restr	0.011	1041

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 (%)
1.46-1.4766	0.2625	191	0.2423	3505	X-RAY DIFFRACTION	99
1.4766-1.494	0.2652	182	0.2216	3532	X-RAY DIFFRACTION	100
1.494-1.5122	0.2743	156	0.2144	3534	X-RAY DIFFRACTION	99
1.5122-1.5313	0.2215	193	0.2061	3533	X-RAY DIFFRACTION	99
1.5313-1.5515	0.2234	207	0.1918	3499	X-RAY DIFFRACTION	100
1.5515-1.5727	0.222	181	0.1853	3525	X-RAY DIFFRACTION	100
1.5727-1.5952	0.1912	167	0.1781	3549	X-RAY DIFFRACTION	99
1.5952-1.619	0.2054	177	0.1678	3530	X-RAY DIFFRACTION	99
1.619-1.6443	0.1859	177	0.1608	3549	X-RAY DIFFRACTION	100
1.6443-1.6713	0.194	184	0.1511	3535	X-RAY DIFFRACTION	100
1.6713-1.7001	0.1655	181	0.1466	3547	X-RAY DIFFRACTION	100
1.7001-1.731	0.1931	180	0.151	3551	X-RAY DIFFRACTION	100
1.731-1.7643	0.17	163	0.1502	3560	X-RAY DIFFRACTION	100
1.7643-1.8003	0.1444	177	0.1436	3553	X-RAY DIFFRACTION	100
1.8003-1.8395	0.1782	162	0.1446	3586	X-RAY DIFFRACTION	100
1.8395-1.8823	0.1695	150	0.1477	3600	X-RAY DIFFRACTION	100
1.8823-1.9293	0.1665	159	0.1438	3612	X-RAY DIFFRACTION	100
1.9293-1.9815	0.1659	172	0.1483	3568	X-RAY DIFFRACTION	100
1.9815-2.0398	0.1696	211	0.1507	3537	X-RAY DIFFRACTION	100
2.0398-2.1056	0.1854	220	0.1482	3531	X-RAY DIFFRACTION	100
2.1056-2.1809	0.1847	232	0.1499	3540	X-RAY DIFFRACTION	100
2.1809-2.2682	0.1751	181	0.1483	3588	X-RAY DIFFRACTION	100
2.2682-2.3714	0.1725	198	0.1555	3598	X-RAY DIFFRACTION	100
2.3714-2.4965	0.1698	223	0.1496	3544	X-RAY DIFFRACTION	100
2.4965-2.6528	0.1629	178	0.1523	3608	X-RAY DIFFRACTION	100
2.6528-2.8576	0.1743	192	0.1492	3628	X-RAY DIFFRACTION	100
2.8576-3.1451	0.1817	187	0.1514	3638	X-RAY DIFFRACTION	100
3.1451-3.6	0.1663	148	0.1455	3684	X-RAY DIFFRACTION	100
3.6-4.5348	0.1504	245	0.1321	3632	X-RAY DIFFRACTION	100
4.5348-42.5851	0.1908	158	0.1694	3883	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	0.3715	0.2594	0.0412	0.3129	-0.0179	0.1474	-0.0358	0.276	-0.0612	-0.0067	0.0396	-0.0665	0.0642	0.1073	0.0001	0.2135	0.0237	0.0178	0.3293	-0.0169	0.1945	25.0151	17.4925	5.9566
2	0.2478	-0.0328	0.3022	0.2227	-0.0612	0.8862	-0.077	0.1806	0.0093	0.0203	0.0571	-0.0036	-0.0235	-0.0174	-0.0001	0.1827	0.0084	-0.0057	0.2761	0.0337	0.173	14.8678	26.7926	10.1813
3	0.2355	-0.0705	0.1062	0.1002	0.1158	0.2246	-0.0012	0.1949	-0.1337	-0.0733	-0.0253	0.1241	0.1194	-0.3397	-0.0024	0.2169	-0.0325	-0.0194	0.4718	0.0485	0.2265	1.8468	22.9701	0.9227
4	0.3901	-0.0385	0.0085	0.097	0.2065	0.3141	0.0338	0.4739	-0.1701	-0.0082	-0.0044	0.1101	0.1574	-0.1687	0.1493	0.2696	-0.0609	-0.013	0.5197	-0.0593	0.2379	4.773	13.4481	-7.8937
5	0.0197	-0.0293	-0.048	0.0122	0.0407	0.0601	-0.0152	0.2824	-0.0998	0.0662	-0.0077	-0.0038	0.4865	-0.1752	0	0.352	-0.0257	0.0016	0.3652	-0.0661	0.2468	17.4761	5.9712	5.636
6	0.3209	0.1169	0.0988	0.1828	-0.1457	0.2576	0.0615	0.3245	0.0595	-0.366	-0.1147	0.0837	-0.1429	0.0624	0.0084	0.2733	-0.0053	-0.0138	0.529	-0.0426	0.1853	14.282	17.0383	-12.9185
7	0.3475	0.2289	-0.274	0.4585	-0.0376	0.2376	0.0032	-0.0851	0.0106	0.0315	-0.0512	-0.1423	-0.03	0.1042	0	0.1786	0.0202	-0.0224	0.1567	0.0214	0.237	27.1132	23.4459	42.5412
8	0.465	0.0187	-0.0082	1.0016	-0.061	0.8269	-0.0066	0.0222	-0.0057	-0.0344	0.0391	-0.0204	0.0098	-0.0169	-0	0.1672	0.0123	-0.0051	0.1208	0.0097	0.2098	18.6526	19.8964	35.5046
9	0.0614	0.0601	0.0065	0.0809	0.0659	0.0909	0.0093	-0.0799	0.2839	0.2554	0.0577	0.2805	-0.0892	-0.397	-0.0001	0.2603	0.0228	0.0612	0.2869	0.0304	0.3212	5.7626	17.192	52.128
10	0.3178	0.1908	-0.0131	0.2331	0.1475	0.128	0.1335	-0.1394	0.0623	0.1865	-0.0756	0.2752	0.0609	-0.2308	-0	0.2455	-0.0001	0.0477	0.2459	-0.0132	0.2504	9.1474	25.4181	54.3988
11	0.1024	0.0929	0.0541	0.0585	0.0451	0.1158	0.0516	-0.0105	0.1534	-0.0318	-0.0404	-0.0127	-0.1483	-0.2169	0.0012	0.2406	0.0522	0.0126	0.1569	-0.0013	0.2431	12.3435	35.3962	39.2054
12	0.429	0.2654	-0.1084	0.2559	-0.2557	0.3128	0.0642	-0.2763	-0.0181	0.3012	-0.0345	-0.017	-0.072	0.2109	0.0008	0.3053	-0.0268	0.0051	0.2082	-0.0347	0.2017	19.2277	25.728	58.0087

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 35 through 92 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 93 through 194 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 195 through 236 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 237 through 298 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 299 through 330 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 331 through 363 )
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 34 through 63 )
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 64 through 225 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 226 through 246 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 247 through 298 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 299 through 330 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 331 through 362 )

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