PDB-8zu5: Crystal Structure of Methyl parathion hydrolase mutant A66D/I143V...

ID or keywords:

Entry

Database: PDB / ID: 8zu5

Title

Crystal Structure of Methyl parathion hydrolase mutant A66D/I143V/I145L/Q272D/S279A/

Components

Methyl parathion hydrolase

Keywords

HYDROLASE

Function / homology

: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / hydrolase activity / metal ion binding / Methyl parathion hydrolase

Function and homology information

Biological species

Pseudomonas sp. WBC-3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Xu, F. / Fan, S.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Methyl parathion hydrolase mutant A66D/I143V/I145L/Q272D/S279A/
Authors: Xu, F. / Fan, S. / Li, Y.

History

Deposition	Jun 7, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zu5.cif.gz	241.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8zu5.ent.gz	193.1 KB	Display	PDB format
PDBx/mmJSON format	8zu5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/8zu5 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/8zu5	HTTPS FTP

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Related structure data

Similar structure data	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	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Methyl parathion hydrolase

B: Methyl parathion hydrolase

hetero molecules

62.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	58.801, 83.719, 115.492
Angle α, β, γ (deg.)	90.00, 94.33, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Methyl parathion hydrolase Mass: 31219.289 Da / Num. of mol.: 2 / Mutation: A66D, I143V, I145L, Q272D, S279A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. WBC-3 (bacteria) / Gene: mpd / Production host: Escherichia coli (E. coli) / References: UniProt: Q841S6
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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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: 45.81 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350,0.1 M Tris pH 8.6, 0.2 M NaCl

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL02U1 / Wavelength: 0.9781 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 16, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9781 Å / Relative weight: 1

Reflection

Resolution: 1.83→50 Å / Num. obs: 48782 / % possible obs: 98.8 % / Redundancy: 5.5 % / CC_1/2: 0.953 / CC star: 0.988 / R_merge(I) obs: 0.184 / R_pim(I) all: 0.086 / R_rim(I) all: 0.204 / Χ²: 1.828 / Net I/σ(I): 4.5 / Num. measured all: 269800

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.83-1.86	5.1	0.851	2386	0.782	0.937	0.407	0.947	0.734	99.1
1.86-1.9	5.3	0.728	2482	0.818	0.949	0.337	0.805	0.859	99.8
1.9-1.93	5.5	0.698	2394	0.838	0.955	0.32	0.77	0.975	99.2
1.93-1.97	5.4	0.602	2489	0.854	0.96	0.277	0.665	1.016	99.1
1.97-2.01	5.5	0.519	2400	0.898	0.973	0.24	0.573	1.066	99.4
2.01-2.06	5.4	0.479	2473	0.908	0.976	0.223	0.531	1.235	99.2
2.06-2.11	5.4	0.467	2429	0.994	0.998	0.223	0.521	1.372	99.2
2.11-2.17	5.2	0.407	2422	0.919	0.979	0.196	0.454	1.392	99.3
2.17-2.23	5.4	0.396	2462	0.928	0.981	0.186	0.439	1.5	99
2.23-2.31	5.9	0.4	2424	0.882	0.968	0.177	0.439	1.673	99.2
2.31-2.39	5.9	0.361	2442	0.952	0.988	0.158	0.396	1.647	99.1
2.39-2.48	5.9	0.313	2425	0.954	0.988	0.139	0.344	1.808	98.5
2.48-2.6	5.8	0.28	2427	0.953	0.988	0.127	0.309	1.909	98.9
2.6-2.73	5.5	0.242	2436	0.958	0.989	0.112	0.268	2.042	98.2
2.73-2.9	5.3	0.204	2424	0.965	0.991	0.097	0.227	2.249	98.4
2.9-3.13	5.9	0.171	2432	0.977	0.994	0.077	0.188	2.552	97.8
3.13-3.44	5.7	0.146	2438	0.975	0.994	0.068	0.161	2.838	98.1
3.44-3.94	5.3	0.127	2441	0.98	0.995	0.062	0.142	3.101	98.2
3.94-4.97	5.5	0.105	2458	0.988	0.997	0.05	0.117	3.221	98.8
4.97-50	5.7	0.108	2498	0.988	0.997	0.05	0.12	3.004	98.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.83→29.32 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2419	2369	4.88 %
R_work	0.2079	-	-
obs	0.2096	48578	98.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.83→29.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4404	0	4	362	4770

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	6.469	622
X-RAY DIFFRACTION	f_chiral_restr	0.073	690
X-RAY DIFFRACTION	f_plane_restr	0.013	804

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 (%)
1.83-1.87	0.3275	137	0.2901	2610	X-RAY DIFFRACTION	96
1.87-1.91	0.2917	136	0.2493	2752	X-RAY DIFFRACTION	99
1.91-1.95	0.2671	139	0.2266	2694	X-RAY DIFFRACTION	98
1.95-2	0.2567	129	0.219	2706	X-RAY DIFFRACTION	99
2-2.05	0.2504	149	0.214	2696	X-RAY DIFFRACTION	99
2.05-2.11	0.261	148	0.2238	2718	X-RAY DIFFRACTION	98
2.11-2.18	0.2566	139	0.2162	2714	X-RAY DIFFRACTION	99
2.18-2.26	0.2718	145	0.2127	2726	X-RAY DIFFRACTION	99
2.26-2.35	0.284	125	0.2153	2749	X-RAY DIFFRACTION	99
2.35-2.46	0.2725	154	0.2223	2706	X-RAY DIFFRACTION	99
2.46-2.59	0.2582	148	0.2104	2698	X-RAY DIFFRACTION	99
2.59-2.75	0.2458	128	0.2154	2717	X-RAY DIFFRACTION	98
2.75-2.96	0.2329	129	0.2184	2752	X-RAY DIFFRACTION	98
2.96-3.26	0.244	134	0.1986	2704	X-RAY DIFFRACTION	98
3.26-3.73	0.2195	142	0.196	2716	X-RAY DIFFRACTION	98
3.73-4.69	0.1856	126	0.1835	2766	X-RAY DIFFRACTION	99
4.69-29.32	0.24	161	0.2011	2785	X-RAY DIFFRACTION	99

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	0.9546	-0.3291	1.5238	2.0599	0.3384	2.7007	0.0141	0.1644	0.0631	-0.0638	0.0685	0.4933	0.7255	-0.5695	0.0048	0.2641	-0.0484	-0.0046	0.2175	0.0282	0.2786	1.8552	-8.738	30.2564
2	0.5058	-0.7437	0.2845	2.1456	-0.022	1.3275	-0.3039	-0.5204	0.3614	0.4349	0.2684	0.3611	-0.384	-0.5573	0.1462	0.3272	0.0947	0.0069	0.5324	-0.1175	0.4079	-5.8359	9.9879	44.574
3	2.0673	0.0274	0.7984	2.7775	-0.317	3.8282	0.1519	-0.1908	-0.2516	0.1683	-0.199	-0.0474	0.1656	-0.1574	0.0195	0.1795	-0.006	-0.0154	0.1286	0.0069	0.1374	9.816	-7.5845	39.9483
4	2.8987	-0.3154	1.0752	1.8093	0.4529	3.6015	0.1337	-0.2647	-0.2139	0.0978	-0.0542	-0.0739	0.426	0.1752	-0.0349	0.1962	0.0243	-0.0018	0.2102	0.0435	0.1595	15.0365	-8.5499	44.5669
5	2.9454	-0.1724	0.9515	2.7842	-0.2673	3.4656	-0.0462	-0.4834	0.1596	0.3742	-0.0015	-0.0211	0.0923	-0.0277	0.0506	0.163	0.0055	-0.027	0.2923	-0.0281	0.1667	17.9841	-0.5961	51.4455
6	2.3475	-0.8224	0.6373	2.0344	0.655	2.8716	-0.1587	-0.1274	0.4295	0.0314	-0.0034	-0.126	-0.4053	0.1927	0.1905	0.1789	-0.001	-0.0334	0.1657	0.0144	0.2259	10.2222	9.7193	37.3671
7	1.8185	1.3053	0.747	6.8678	2.5926	4.2454	-0.154	0.2093	0.6085	0.04	-0.2958	0.8865	-0.5709	0.0182	0.2732	0.248	0.0118	-0.0575	0.1803	0.0182	0.3694	4.2509	8.6986	26.3481
8	1.9294	-0.7908	0.8763	1.0044	0.2264	1.2732	0.0122	-0.3519	0.0654	0.1105	0.1265	-0.0512	0.4888	0.0375	-0.0534	0.2237	-0.0359	-0.0222	0.1689	0.0199	0.1877	-4.1442	-8.2653	24.9773
9	1.8679	-0.5641	0.4567	2.2196	-0.7104	1.7034	-0.124	0.3312	0.575	0.1946	-0.3768	-0.568	-0.0322	0.4221	0.1984	0.258	-0.0612	-0.0476	0.2329	0.0914	0.4443	0.6587	13.3456	9.0877
10	1.279	-0.5552	0.8258	1.1178	0.5358	2.4368	-0.1331	0.3526	0.1041	0.0282	0.1377	-0.3151	0.1026	-0.0003	0.052	0.1571	-0.0135	-0.0076	0.1261	0.0171	0.248	-3.8449	0.0431	17.8063
11	2.9276	-0.451	-0.1986	1.4433	0.4474	1.9178	0.4441	-0.0854	-0.1763	-0.0837	-0.2911	-0.0035	0.0825	-0.0902	-0.0469	0.18	-0.0712	-0.0451	0.1331	0.0003	0.2252	-11.9297	-10.1225	15.4499
12	1.7592	0.7694	0.7025	1.2393	-0.0173	2.3278	0.2555	-0.0521	-0.3036	0.0865	-0.1568	0.0709	0.3791	-0.2044	-0.0144	0.1955	-0.0719	-0.0275	0.1486	0.0066	0.2886	-17.7381	-11.3597	12.7556
13	3.5297	-0.6008	0.4901	3.5859	-0.4019	5.628	-0.1842	0.5647	0.1934	-0.5144	0.0935	-0.1433	0.2471	0.12	0.0492	0.1353	-0.0374	-0.0201	0.2408	0.004	0.2352	-17.0742	-6.7429	-2.7027
14	1.8161	0.3598	0.5784	1.6306	0.2844	1.797	0.0711	-0.2455	0.1277	0.1932	-0.112	0.2483	0.1161	-0.4586	-0.0002	0.1198	-0.0574	0.0274	0.2357	-0.0303	0.2728	-24.8568	-0.8368	17.964
15	2.3795	0.4836	0.8037	1.1153	-0.5593	1.7581	-0.1264	0.013	0.373	-0.0605	0.158	-0.1113	-0.1927	-0.1406	0.1217	0.1858	-0.0342	0.0168	0.1539	-0.0171	0.314	-10.1765	10.6749	11.8338
16	2.175	0.2072	1.0393	1.2754	-0.3489	1.9633	-0.0087	-0.163	0.4098	0.077	-0.1047	0.2351	-0.23	-0.179	0.1031	0.1659	-0.019	0.0057	0.1828	-0.044	0.3081	-15.0149	8.939	19.7688
17	2.6835	-0.9948	1.4117	4.1243	-1.8606	3.7252	-0.1526	-0.4369	0.5248	0.1899	-0.0158	-0.2661	-0.3841	-0.3328	0.102	0.1954	-0.0288	0.0263	0.2396	-0.0409	0.2943	-8.6821	8.2457	29.395

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 36 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 97 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 98 through 125 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 179 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 180 through 238 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 239 through 308 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 309 through 329 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 36 through 67 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 68 through 87 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 88 through 103 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 104 through 125 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 126 through 179 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 180 through 209 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 210 through 252 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 253 through 276 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 277 through 308 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 309 through 329 )

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