PDB-8wbp: Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] muta...

ID or keywords:

Entry

Database: PDB / ID: 8wbp

Title

Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant E212Q

Components

Epoxide hydrolase

Keywords

HYDROLASE / cis-Epoxysuccinate Hydrolases / epoxide hydrolase / L(+)-tartaric acid

Function / homology

hydrolase activity, acting on acid halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Epoxide hydrolase

Function and homology information

Biological species

Rhodococcus opacus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Dong, S. / Xuan, J.S. / Feng, Y.G. / Cui, Q.

Funding support

China, 1items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Deciphering the stereo-specific catalytic mechanisms of cis-epoxysuccinate hydrolases producing L(+)-tartaric acid.
Authors: Dong, S. / Xuan, J. / Feng, Y. / Cui, Q.

History

Deposition	Sep 10, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 31, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wbp.cif.gz	208.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbp.ent.gz	166.1 KB	Display	PDB format
PDBx/mmJSON format	8wbp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wbp_validation.pdf.gz	439.8 KB	Display	wwPDB validaton report
Full document	8wbp_full_validation.pdf.gz	445.3 KB	Display
Data in XML	8wbp_validation.xml.gz	22.3 KB	Display
Data in CIF	8wbp_validation.cif.gz	32.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/8wbp ftp://data.pdbj.org/pub/pdb/validation_reports/wb/8wbp	HTTPS FTP

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Related structure data

Related structure data	8wbkC 8wblC 8wbmC 8wbnC 8wboC 8wbqC 8wbrC 8wbsC 8wbtC C: citing same article (ref.)
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	#220 - Apr 2018 Dehalogenases similarity (3) #118 - Oct 2009 Sodium-Potassium Pump similarity (1)

Deposited unit

A: Epoxide hydrolase

B: Epoxide hydrolase

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	43.162, 57.929, 62.956
Angle α, β, γ (deg.)	68.30, 74.57, 83.03
Int Tables number	1
Space group name H-M	P1

#1: Protein	Epoxide hydrolase Mass: 29350.924 Da / Num. of mol.: 2 / Mutation: E212Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus opacus (bacteria) / Gene: eph / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1KLR5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.4 Å³/Da / Density % sol: 48.77 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M sodium citrate tribasic, 0.2M potassium acetate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.87→53.8 Å / Num. obs: 76307 / % possible obs: 93.3 % / Redundancy: 3.4 % / CC_1/2: 0.996 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.035 / R_rim(I) all: 0.065 / Χ²: 0.91 / Net I/σ(I): 12.2
Reflection shell	Resolution: 1.87→1.98 Å / % possible obs: 85.3 % / Redundancy: 3.1 % / R_merge(I) obs: 0.247 / Num. measured all: 19171 / Num. unique obs: 6226 / CC_1/2: 0.954 / R_pim(I) all: 0.169 / R_rim(I) all: 0.302 / Χ²: 0.62 / Net I/σ(I) obs: 3.6

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Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	v1.21	refinement
autoPROC		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.87→41.59 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1968	3648	4.78 %
R_work	0.1684	-	-
obs	0.1698	76307	84.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.87→41.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3711	0	0	329	4040

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3807
X-RAY DIFFRACTION	f_angle_d	1.054	5174
X-RAY DIFFRACTION	f_dihedral_angle_d	19.617	530
X-RAY DIFFRACTION	f_chiral_restr	0.053	575
X-RAY DIFFRACTION	f_plane_restr	0.009	672

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 (%)
1.87-1.89	0.2918	75	0.2633	1487	X-RAY DIFFRACTION	45
1.89-1.92	0.286	141	0.2486	2855	X-RAY DIFFRACTION	89
1.92-1.95	0.2501	155	0.2211	3012	X-RAY DIFFRACTION	89
1.95-1.98	0.2399	146	0.2029	2890	X-RAY DIFFRACTION	89
1.98-2.01	0.2421	147	0.2019	2927	X-RAY DIFFRACTION	89
2.01-2.04	0.2308	143	0.1939	2943	X-RAY DIFFRACTION	88
2.04-2.08	0.2405	148	0.1909	2918	X-RAY DIFFRACTION	89
2.08-2.11	0.1737	147	0.1831	2937	X-RAY DIFFRACTION	89
2.11-2.15	0.2718	146	0.1832	2953	X-RAY DIFFRACTION	89
2.15-2.2	0.2296	150	0.1877	2973	X-RAY DIFFRACTION	90
2.2-2.25	0.2383	148	0.1824	2966	X-RAY DIFFRACTION	89
2.25-2.3	0.2197	142	0.1903	2877	X-RAY DIFFRACTION	88
2.3-2.36	0.2568	142	0.1847	2909	X-RAY DIFFRACTION	88
2.36-2.42	0.198	144	0.1971	2961	X-RAY DIFFRACTION	89
2.42-2.49	0.2431	143	0.1837	2886	X-RAY DIFFRACTION	88
2.49-2.57	0.2505	148	0.1907	2833	X-RAY DIFFRACTION	86
2.57-2.66	0.2429	144	0.1888	2907	X-RAY DIFFRACTION	87
2.66-2.77	0.2076	151	0.183	2822	X-RAY DIFFRACTION	86
2.77-2.9	0.2529	139	0.1816	2820	X-RAY DIFFRACTION	84
2.9-3.05	0.2352	140	0.1798	2764	X-RAY DIFFRACTION	84
3.05-3.24	0.1541	138	0.1709	2755	X-RAY DIFFRACTION	84
3.24-3.49	0.1639	135	0.1641	2627	X-RAY DIFFRACTION	80
3.49-3.84	0.1767	138	0.1353	2749	X-RAY DIFFRACTION	83
3.84-4.4	0.1842	135	0.1415	2682	X-RAY DIFFRACTION	81
4.4-5.54	0.1424	133	0.14	2656	X-RAY DIFFRACTION	80
5.54-41.59	0.1667	130	0.1575	2550	X-RAY DIFFRACTION	77

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	5.1423	2.4205	-2.199	4.3547	-5.3947	7.2728	-0.3124	-0.0125	-0.8051	-0.526	-0.0136	-0.5563	0.6813	0.4961	0.2935	0.2859	0.0491	0.0402	0.4269	-0.007	0.3963	-4.0768	16.4294	-51.1221
2	9.5975	3.169	-6.1756	1.6195	-1.6276	4.7252	-0.0272	0.0976	0.2394	-0.1161	0.0276	-0.0819	-0.1725	0.0721	0.0168	0.2999	0.0035	-0.0135	0.2802	0.0158	0.2942	-15.5452	26.5317	-47.1322
3	2.2892	0.611	-1.3541	2.8569	-0.6033	5.4167	0.0259	0.1268	0.0235	-0.1599	0.025	-0.1564	-0.0201	0.0968	-0.1114	0.2144	0.0174	-0.0305	0.2452	0.0014	0.2321	-18.6603	19.3138	-37.3155
4	6.3931	-0.5754	-0.0954	3.9054	0.6689	6.2131	0.0315	-0.0076	-0.3785	-0.031	0.0034	-0.1517	0.4227	0.0668	-0.0373	0.1955	0.0007	-0.0411	0.1618	0.0376	0.165	-17.0054	10.6265	-37.166
5	6.4434	-0.8865	1.505	7.8237	-4.627	2.895	0.0454	0.255	-0.6378	-0.2664	-0.2194	-0.265	0.6881	0.334	0.1265	0.3513	-0.0048	-0.018	0.2328	-0.0635	0.3263	-25.1959	6.0749	-42.1963
6	2.5733	3.5182	-1.114	8.0752	-4.1962	3.7528	-0.2712	0.4957	0.1048	-1.0456	0.2763	0.1729	0.3458	-0.0916	0.0026	0.3773	0.0057	-0.0128	0.3357	-0.0427	0.247	-29.3382	14.2005	-53.0553
7	2.4988	2.9552	-1.4821	7.207	1.8139	8.7659	0.2112	0.1875	0.293	-0.0593	-0.1102	0.6408	-0.2471	-0.7702	-0.0081	0.1634	0.0229	-0.0268	0.3221	-0.0242	0.2488	-37.2944	17.2696	-40.6933
8	6.0171	4.7653	-5.6879	7.238	-5.2742	5.6891	0.183	-0.3815	-0.2706	0.1683	-0.2693	-0.6991	-0.3275	0.5391	-0.0362	0.3077	-0.0369	-0.011	0.3192	-0.0417	0.3846	-11.9795	25.2195	-20.2121
9	7.7557	5.4767	-2.4848	4.6584	-3.3532	4.4878	-0.1051	-0.0021	0.1175	0.1929	0.2292	0.7062	-0.0468	-0.5841	-0.1536	0.3857	0.0034	0.0432	0.3027	-0.0316	0.3493	-28.762	11.7124	-4.6091
10	3.1981	-1.3237	-2.8449	4.4908	-0.3	7.0155	0.1947	-0.8676	0.0318	0.3141	-0.1852	-0.5367	-0.1312	0.7879	0.0212	0.3684	-0.0691	-0.0955	0.4367	0.059	0.3665	-14.5041	8.8566	-5.7927
11	5.0776	3.8491	-5.1555	5.5154	-2.6357	8.6175	-0.3672	-0.2803	-0.6685	-0.1371	-0.2835	-0.7726	0.3893	0.6573	0.5396	0.2968	0.0434	-0.0087	0.2346	0.0621	0.3614	-15.3371	2.3055	-12.0381
12	7.9686	3.799	-1.6076	6.8205	-2.2375	4.4896	-0.068	-0.1451	-0.3404	0.1973	-0.0081	0.1046	0.2158	-0.3235	0.0757	0.2839	-0.0037	-0.0085	0.2475	0.0079	0.2893	-26.312	3.232	-7.7691
13	7.4876	4.0112	-5.3145	6.3852	-5.7545	8.6877	0.1287	0.4505	0.5149	-0.1817	0.3418	0.5449	-0.2665	-0.6148	-0.5594	0.3618	0.0336	-0.0801	0.315	-0.019	0.254	-21.293	27.7663	-19.8933
14	1.7219	-0.2063	-0.1993	2.8464	-0.6478	2.9289	-0.0576	-0.0725	0.0199	-0.1011	0.0287	-0.259	0.0236	0.2811	0.028	0.2485	-0.0129	-0.0145	0.2497	-0.0319	0.2343	-12.3831	17.4136	-24.7255
15	2.9981	-0.2524	-3.2945	3.9681	-1.4142	7.412	0.149	-0.322	-0.0731	0.1292	-0.0048	-0.5331	0.1579	0.8487	-0.1436	0.2885	-0.0428	-0.0407	0.42	-0.0853	0.4199	-3.1168	23.6911	-20.0172
16	5.1324	2.4819	-2.7149	3.3916	0.2506	5.3387	0.3351	-0.6418	0.2207	0.4955	-0.203	-0.1926	-0.5856	0.6741	-0.0924	0.401	-0.0513	-0.049	0.3398	-0.0992	0.3829	-10.3184	30.5361	-11.9514
17	3.4308	3.544	-5.0972	4.4324	-4.3754	9.7601	-0.1261	-0.1572	-0.2527	-0.1987	0.0766	-0.0751	0.7263	0.1364	0.064	0.2469	0.0054	-0.0123	0.2488	0.0108	0.2894	-25.6937	14.9646	-40.6273
18	5.3616	2.1797	-0.2579	7.5583	0.97	7.9325	-0.4373	0.8481	1.0249	-0.6276	0.5207	0.3094	-0.8666	-0.2332	-0.2076	0.3605	-0.0053	-0.0111	0.3733	0.1113	0.358	-12.583	32.2046	-55.9603
19	2.9417	-1.7482	1.6722	4.0797	-3.9812	4.13	-0.022	0.4789	-0.4073	-0.6085	0.1529	0.5278	0.6455	-0.1755	-0.2105	0.4083	-0.0504	0.0144	0.4649	-0.0419	0.3191	-11.5204	18.2695	-56.8747

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 68 through 88 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 89 through 125 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 126 through 147 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 148 through 177 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 178 through 200 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 201 through 227 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 228 through 247 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 11 through 25 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 26 through 43 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 44 through 68 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 69 through 88 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 89 through 108 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 109 through 125 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 126 through 177 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 178 through 200 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 201 through 246 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 11 through 25 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 26 through 43 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 44 through 67 )

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