PDB-4zwu: Crystal structure of organophosphate anhydrolase/prolidase mutant...

ID or keywords:

Entry

Database: PDB / ID: 4zwu

Title

Crystal structure of organophosphate anhydrolase/prolidase mutant Y212F, V342L, I215Y

Components

ORGANOPHOSPHATE ANHYDROLASE/PROLIDASE

Keywords

HYDROLASE / OPAA organophosphate prolidase anhydrolase

Function / homology

Function and homology information

diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / Xaa-Pro dipeptidase / proline dipeptidase activity / aryldialkylphosphatase / aryldialkylphosphatase activity / metalloexopeptidase activity / aminopeptidase activity / response to toxic substance / proteolysis ...
Similarity search - Function

Biological species

Alteromonas sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.2 Å

Authors

Daczkowski, C.M. / Pegan, S.D. / Harvey, S.P.

Citation

Journal: Biochemistry / Year: 2015
Title: Engineering the Organophosphorus Acid Anhydrolase Enzyme for Increased Catalytic Efficiency and Broadened Stereospecificity on Russian VX.
Authors: Daczkowski, C.M. / Pegan, S.D. / Harvey, S.P.

History

Deposition	May 19, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2015	Group: Database references
Revision 1.2	Dec 2, 2020	Group: Database references / Derived calculations Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4zwu.cif.gz	372.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4zwu.ent.gz	306 KB	Display	PDB format
PDBx/mmJSON format	4zwu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4zwu_validation.pdf.gz	454.8 KB	Display	wwPDB validaton report
Full document	4zwu_full_validation.pdf.gz	456.9 KB	Display
Data in XML	4zwu_validation.xml.gz	35.5 KB	Display
Data in CIF	4zwu_validation.cif.gz	51.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zw/4zwu ftp://data.pdbj.org/pub/pdb/validation_reports/zw/4zwu	HTTPS FTP

-
Related structure data

Related structure data	4zwoC 4zwpC C: citing same article (ref.)
Similar structure data	3rva-1 4qr8-d 4zwo-d 7e5c-1 6ah7-2 6ah7-1 6sre-d 6qsc-d 5mc3-d 2okn-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ORGANOPHOSPHATE ANHYDROLASE/PROLIDASE

B: ORGANOPHOSPHATE ANHYDROLASE/PROLIDASE

hetero molecules

102 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)	102.890, 68.846, 139.394
Angle α, β, γ (deg.)	90.00, 109.58, 90.00
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 2 molecules AB

#1: Protein	ORGANOPHOSPHATE ANHYDROLASE/PROLIDASE / X-Pro dipeptidase / DFPase / Imidodipeptidase / Organophosphorus acid anhydrolase 2 / OPAA-2 / ...X-Pro dipeptidase / DFPase / Imidodipeptidase / Organophosphorus acid anhydrolase 2 / OPAA-2 / Paraoxon hydrolase / Phosphotriesterase / Proline dipeptidase / Prolidase Mass: 50453.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas sp. (bacteria) / Gene: pepQ, opaA / Plasmid: pSE420 / Production host: Escherichia coli (E. coli) References: UniProt: Q44238, Xaa-Pro dipeptidase, EC: 3.1.8.2, aryldialkylphosphatase

#1: Protein

ORGANOPHOSPHATE ANHYDROLASE/PROLIDASE / X-Pro dipeptidase / DFPase / Imidodipeptidase / Organophosphorus acid anhydrolase 2 / OPAA-2 / ...

Mass: 50453.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Alteromonas sp. (bacteria) / Gene: pepQ, opaA / Plasmid: pSE420 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q44238, Xaa-Pro dipeptidase, EC: 3.1.8.2, aryldialkylphosphatase

-
Non-polymers , 5 types, 480 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-BA / BARIUM ION Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#4: Chemical	ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₃
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.78 % / Description: Flat square plates
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4% PEG 4,000, 20% Isopropanol, 11 mM BaCl2

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 46682 / % possible obs: 98.7 % / Redundancy: 4.5 % / B_iso Wilson estimate: 36.43 Å² / R_merge(I) obs: 0.083 / R_pim(I) all: 0.042 / R_rim(I) all: 0.094 / Χ²: 1.104 / Net I/av σ(I): 18.307 / Net I/σ(I): 8.8 / Num. measured all: 209219

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	2.8	0.284	1941	0.909	0.182	0.34	0.609	82.8
2.24-2.28	3.4	0.282	2187	0.936	0.165	0.328	0.648	94.4
2.28-2.32	3.6	0.285	2338	0.937	0.161	0.329	0.664	98.6
2.32-2.37	3.9	0.268	2362	0.949	0.146	0.306	0.703	99.4
2.37-2.42	4.2	0.265	2284	0.963	0.139	0.3	0.748	99.7
2.42-2.48	4.4	0.247	2406	0.968	0.127	0.279	0.806	99.7
2.48-2.54	4.6	0.234	2297	0.971	0.118	0.263	0.843	99.7
2.54-2.61	4.7	0.217	2364	0.975	0.108	0.243	0.878	100
2.61-2.69	4.8	0.189	2374	0.98	0.094	0.212	0.93	100
2.69-2.77	4.8	0.175	2332	0.981	0.087	0.196	1.074	100
2.77-2.87	4.8	0.151	2359	0.984	0.076	0.169	1.146	100
2.87-2.99	4.9	0.132	2364	0.986	0.066	0.148	1.3	100
2.99-3.12	4.8	0.117	2383	0.99	0.059	0.131	1.307	100
3.12-3.29	4.8	0.101	2356	0.992	0.051	0.113	1.29	100
3.29-3.49	4.8	0.089	2359	0.992	0.045	0.1	1.46	100
3.49-3.76	4.8	0.078	2346	0.993	0.039	0.087	1.501	100
3.76-4.14	4.8	0.072	2411	0.995	0.036	0.081	1.565	100
4.14-4.74	4.8	0.066	2369	0.995	0.033	0.074	1.287	100
4.74-5.97	4.8	0.059	2390	0.996	0.029	0.066	1.238	100
5.97-50	4.7	0.046	2460	0.998	0.024	0.052	1.215	99.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data collection
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 2.2→48.47 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2189	2355	5.05 %
R_work	0.17	-	-
obs	0.1724	46672	98.52 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→48.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7050	0	19	470	7539

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7260
X-RAY DIFFRACTION	f_angle_d	0.604	9853
X-RAY DIFFRACTION	f_dihedral_angle_d	12.39	2621
X-RAY DIFFRACTION	f_chiral_restr	0.024	1034
X-RAY DIFFRACTION	f_plane_restr	0.003	1306

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 (%)
2.1918-2.2365	0.2585	94	0.2304	2148	X-RAY DIFFRACTION	81
2.2365-2.2852	0.2844	123	0.2191	2551	X-RAY DIFFRACTION	96
2.2852-2.3383	0.2879	156	0.2118	2550	X-RAY DIFFRACTION	99
2.3383-2.3968	0.2699	152	0.2015	2639	X-RAY DIFFRACTION	100
2.3968-2.4616	0.2257	130	0.2069	2641	X-RAY DIFFRACTION	100
2.4616-2.534	0.2878	124	0.2073	2584	X-RAY DIFFRACTION	100
2.534-2.6158	0.2495	118	0.201	2674	X-RAY DIFFRACTION	100
2.6158-2.7093	0.2385	157	0.2036	2617	X-RAY DIFFRACTION	100
2.7093-2.8178	0.2659	131	0.2035	2661	X-RAY DIFFRACTION	100
2.8178-2.946	0.2502	143	0.2009	2634	X-RAY DIFFRACTION	100
2.946-3.1013	0.2471	137	0.1986	2662	X-RAY DIFFRACTION	100
3.1013-3.2956	0.2356	146	0.1967	2619	X-RAY DIFFRACTION	100
3.2956-3.5499	0.2219	164	0.1716	2611	X-RAY DIFFRACTION	100
3.5499-3.907	0.1946	135	0.1564	2664	X-RAY DIFFRACTION	100
3.907-4.4721	0.1681	150	0.139	2652	X-RAY DIFFRACTION	100
4.4721-5.633	0.2009	149	0.1276	2681	X-RAY DIFFRACTION	100
5.633-48.4817	0.1932	146	0.1417	2729	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	7.1717	-2.5302	2.0768	5.0963	-4.4694	3.9709	0.1134	-0.6149	0.5299	0.7008	0.0618	-0.2455	-0.2569	0.0056	-0.0511	0.4357	-0.0502	-0.042	0.3758	-0.0711	0.4386	84.4409	-7.5993	448.535
2	0.9737	0.8371	-0.2725	3.7086	1.3444	1.2212	0.0203	-0.0846	0.084	-0.3082	0.0377	-0.3319	-0.0976	0.1607	-0.0869	0.2577	0.0144	-0.0232	0.3349	0.0172	0.3636	85.4187	-20.4782	433.9716
3	2.9705	-1.3008	-0.9817	2.4883	0.7669	3.7083	0.1195	-0.0927	-0.1215	-0.0003	0.027	-0.3197	0.4197	0.4807	-0.1468	0.3133	0.0084	-0.0758	0.4407	-0.0398	0.4272	87.7668	-22.8575	444.2062
4	3.9812	1.2381	1.6956	1.1282	0.882	1.6274	-0.0024	0.122	0.04	-0.0457	0.0243	-0.0326	-0.0795	-0.0654	-0.0192	0.3176	0.0405	0.062	0.3104	0.0291	0.2767	59.1025	-13.061	428.2122
5	3.1904	0.7957	0.2494	1.0899	0.7896	1.4715	0.1202	-0.3049	0.1907	0.1963	-0.1905	0.1785	-0.0036	-0.4103	0.0614	0.3251	0.0118	0.0466	0.3369	-0.0248	0.2816	49.9902	-12.8467	443.5333
6	5.1772	1.3893	6.6933	2.4512	1.6691	8.6139	0.3379	-0.9391	-1.1433	0.5375	0.1081	0.2671	0.7616	-0.7622	-0.5089	0.6246	-0.0243	0.0534	0.702	0.1426	0.6104	63.6406	-20.8924	455.9712
7	3.6507	1.8292	0.7927	2.459	0.7826	1.2264	0.1554	-0.1757	0.0789	0.1814	-0.1211	0.1196	0.0808	-0.2186	-0.0349	0.2957	0.0186	0.0599	0.3331	-0.0184	0.2476	49.4397	-13.8517	443.4616
8	6.911	-3.6655	3.7463	4.723	-1.1804	5.2822	0.3449	0.3941	-0.7508	-0.0972	-0.1208	0.3298	0.5981	-0.1636	-0.2561	0.4426	-0.1331	0.0114	0.3482	0.0209	0.3716	62.0652	-52.8403	412.808
9	1.9651	0.9658	0.7703	0.6598	0.4487	1.4026	0.0733	-0.1952	-0.0802	0.2534	-0.1689	-0.002	0.4642	-0.4612	0.1091	0.4045	-0.0537	-0.0095	0.3135	0.0587	0.2785	66.7568	-39.4905	429.0389
10	0.6754	-0.2122	0.2769	0.4565	1.5247	5.7071	-0.0999	0.0857	0.072	0.163	-0.0147	0.3289	0.1087	-0.7602	0.1128	0.5434	-0.1357	0.0659	0.482	0.0593	0.4264	54.224	-44.6826	427.1242
11	2.9093	-0.5031	0.476	1.6294	-0.1493	3.1958	0.0465	-0.5496	-0.3447	0.5882	0.0552	-0.0685	0.6548	-0.0199	-0.0428	0.5872	-0.0773	-0.0725	0.3031	0.0402	0.3555	69.4163	-50.5571	428.8157
12	1.4672	1.2051	-0.4635	3.5174	-0.2465	0.7587	0.0787	0.0176	0.0817	0.0009	-0.0197	0.0751	-0.091	-0.1227	-0.0681	0.2521	0.0301	0.0219	0.312	0.0053	0.2759	69.5593	-20.6678	411.2661
13	1.2205	0.4957	-0.3985	0.845	-0.0786	0.7031	0.0221	0.1674	0.0242	0.0084	0.0433	-0.0522	-0.0503	-0.0295	-0.0452	0.2659	0.0078	0.0118	0.2901	-0.0069	0.2873	82.6921	-27.1927	400.9736
14	4.209	4.18	-0.6266	4.75	-2.8124	8.8417	0.3737	-0.6162	-0.2722	0.7631	-0.6688	-1.0583	0.2613	1.672	0.4582	0.5512	0.1303	-0.0871	0.7152	0.0308	0.7204	88.1005	-44.9887	409.0744
15	3.8245	2.7655	-0.0807	3.7519	0.1317	1.1763	-0.0498	0.2282	0.1713	-0.0175	0.114	0.0813	-0.0704	0.0448	-0.0633	0.2531	0.0317	0.0147	0.2955	0.0011	0.2098	83.4881	-26.9875	401.5216

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 100 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 101 through 161 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 162 through 233 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 234 through 349 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 350 through 370 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 371 through 440 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 25 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 26 through 68 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 69 through 109 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 110 through 161 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 162 through 233 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 234 through 349 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 350 through 369 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 370 through 440 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

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

-
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, 2 molecules AB

-
Non-polymers , 5 types, 480 molecules

-
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

-
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, 2 molecules AB

-Non-polymers , 5 types, 480 molecules

-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

-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, 2 molecules AB

-
Non-polymers , 5 types, 480 molecules

-
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

-
Yorodumi