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

ID or keywords:

Entry

Database: PDB / ID: 8wbm

Title

Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant D193A complexed with sulfate ions

Components

Epoxide hydrolase

Keywords

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

Function / homology

hydrolase activity, acting on 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: 2.06 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	8wbm.cif.gz	209.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbm.ent.gz	167.2 KB	Display	PDB format
PDBx/mmJSON format	8wbm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wbm_validation.pdf.gz	451.6 KB	Display	wwPDB validaton report
Full document	8wbm_full_validation.pdf.gz	455 KB	Display
Data in XML	8wbm_validation.xml.gz	23.4 KB	Display
Data in CIF	8wbm_validation.cif.gz	34.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/8wbm ftp://data.pdbj.org/pub/pdb/validation_reports/wb/8wbm	HTTPS FTP

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Related structure data

Related structure data	8wbkC 8wblC 8wbnC 8wboC 8wbpC 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

hetero molecules

58.8 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)	44.260, 59.490, 64.370
Angle α, β, γ (deg.)	68.23, 75.27, 83.44
Int Tables number	1
Space group name H-M	P1

#1: Protein	Epoxide hydrolase Mass: 29307.900 Da / Num. of mol.: 2 / Mutation: D193A 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: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.6 Å³/Da / Density % sol: 52.63 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.05M ammonium sulfate, 0.05M Bis-tris pH6.5, 30% pentaerythritol ethoxylate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.06→58.18 Å / Num. obs: 34339 / % possible obs: 94.7 % / Redundancy: 3.7 % / CC_1/2: 0.986 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.065 / R_rim(I) all: 0.124 / Net I/σ(I): 8.6 / Num. measured all: 125621
Reflection shell	Resolution: 2.06→2.12 Å / % possible obs: 94.4 % / Redundancy: 3.8 % / R_merge(I) obs: 0.272 / Num. measured all: 9712 / Num. unique obs: 2566 / CC_1/2: 0.935 / R_pim(I) all: 0.164 / R_rim(I) all: 0.319 / Net I/σ(I) obs: 4.1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.06→25.93 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2382	1999	5.83 %
R_work	0.2005	-	-
obs	0.2028	34297	94.6 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.06→25.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3718	0	10	438	4166

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3828
X-RAY DIFFRACTION	f_angle_d	0.984	5201
X-RAY DIFFRACTION	f_dihedral_angle_d	9.47	532
X-RAY DIFFRACTION	f_chiral_restr	0.05	574
X-RAY DIFFRACTION	f_plane_restr	0.008	675

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 (%)
2.06-2.12	0.2631	144	0.2147	2318	X-RAY DIFFRACTION	94
2.12-2.17	0.2694	144	0.2429	2341	X-RAY DIFFRACTION	97
2.17-2.24	0.3707	143	0.2929	2306	X-RAY DIFFRACTION	94
2.24-2.31	0.4673	132	0.3863	2141	X-RAY DIFFRACTION	89
2.31-2.39	0.3226	145	0.2631	2337	X-RAY DIFFRACTION	95
2.39-2.49	0.2478	148	0.2073	2389	X-RAY DIFFRACTION	97
2.49-2.6	0.2354	144	0.1958	2334	X-RAY DIFFRACTION	96
2.6-2.74	0.2449	145	0.199	2338	X-RAY DIFFRACTION	97
2.74-2.91	0.2549	147	0.1984	2370	X-RAY DIFFRACTION	97
2.91-3.13	0.2288	145	0.1952	2346	X-RAY DIFFRACTION	96
3.13-3.45	0.1977	143	0.1787	2318	X-RAY DIFFRACTION	96
3.45-3.94	0.2087	143	0.1737	2308	X-RAY DIFFRACTION	94
3.94-4.96	0.1681	142	0.1391	2296	X-RAY DIFFRACTION	94
4.96-25.93	0.187	134	0.1692	2156	X-RAY DIFFRACTION	89

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	2.1094	1.4578	-2.0038	1.1445	-1.2716	1.9208	-0.1162	-0.9857	-0.1928	0.165	-0.4726	-0.3666	-0.3395	0.6788	-0.3098	0.254	-0.0886	-0.038	0.5504	-0.2013	0.194	44.1351	-9.3784	49.7027
2	1.9471	0.9088	0.2215	0.9842	-0.8803	3.1453	0.0411	-0.1043	0.5334	0.3698	0.3061	0.0175	-1.1661	-0.2885	-0.051	0.4267	-0.0428	0.008	0.2101	-0.0998	0.2462	40.1922	0.8395	38.6798
3	3.2625	2.2868	-2.0908	4.3074	-3.016	4.1648	-0.0546	-0.0515	-0.066	-0.2329	0.0331	0.1588	0.4386	-0.0462	0.033	0.1411	-0.0232	0.0167	0.1338	-0.0267	0.1252	27.1127	-21.3783	15.6366
4	1.7788	0.4689	-0.4789	1.1953	0.0951	1.5121	-0.3221	0.5833	0.8017	-0.3114	0.2388	-0.0451	-0.5568	0.1983	-0.0141	0.3042	-0.0785	-0.0225	0.28	0.1512	0.319	40.5	-3.1995	-0.0429
5	1.9066	0.1114	0.2126	4.908	-1.3558	2.1479	-0.176	0.4554	-0.1223	-0.4939	0.3384	0.496	0.3481	-0.1964	0.0091	0.2414	-0.0354	0.0501	0.4011	-0.0327	0.1561	41.3037	-17.3393	-0.9988
6	1.7531	0.6196	0.0263	1.5455	-0.3054	1.347	-0.1397	0.2054	0.0126	-0.1364	0.0432	-0.2273	0.0138	0.3425	0.0925	0.1455	0.0015	0.0544	0.2744	-0.0068	0.2121	49.0542	-13.6619	3.3136
7	2.8248	0.1776	-1.1379	1.4289	-0.2823	2.5052	0.2048	-0.0223	0.225	0.2446	-0.1578	-0.0377	-0.7916	-0.3405	-0.0927	0.1888	0.024	-0.0429	0.1707	-0.0211	0.1516	25.1403	-11.3282	16.0616
8	1.5155	0.1093	-0.0085	0.3402	-0.2671	1.4584	-0.0001	0.1051	-0.1515	-0.0895	-0.0259	-0.0223	0.1709	-0.016	0.0185	0.1336	-0.0066	0.0005	0.1299	-0.0183	0.114	32.9249	-24.5017	17.5576
9	0.8333	0.6245	0.0367	1.6415	-0.2722	0.4134	-0.0527	0.4023	0.0395	-0.196	0.0024	0.2785	0.0188	-0.5855	0.0502	0.1775	-0.0113	-0.0487	0.233	-0.0432	0.1296	19.8692	-21.1416	8.045
10	4.2702	1.6623	-3.4566	3.3326	-2.5359	5.9711	0.1885	-0.2201	0.0319	0.1368	-0.1111	-0.3789	-0.1953	0.4246	-0.0344	0.1273	-0.0062	-0.0066	0.1646	-0.0421	0.1753	41.1651	-10.8022	36.378
11	2.1304	1.548	0.4113	3.5487	-0.5416	1.2865	0.1972	-0.5449	-0.0884	0.4427	-0.1399	0.3093	-0.0237	-0.1532	-0.0771	0.2334	-0.0632	0.0125	0.4025	-0.0102	0.1764	23.6455	-24.4212	52.4784
12	3.0706	-0.0834	-0.9533	1.9514	0.0493	2.4236	0.3659	-0.8447	0.1256	0.4711	-0.1854	-0.5329	-0.1007	0.3173	0.0283	0.2487	-0.0333	-0.0537	0.2688	0.0547	0.1503	37.6634	-26.8437	51.6025
13	0.7259	0.473	-0.8804	0.858	-0.2194	2.1822	-0.0917	-0.0921	-0.5773	-0.2098	-0.1995	-0.4692	0.7485	0.3066	0.1151	0.2349	0.0274	0.027	0.1461	0.1035	0.3031	38.0523	-33.915	44.7209
14	0.9556	0.5487	-0.0697	1.6968	-0.4969	1.2807	0.1145	-0.1692	-0.2736	0.0122	-0.1222	0.0594	0.1822	-0.1061	-0.0232	0.2591	-0.0706	0.02	0.2299	0.0746	0.1926	26.072	-33.093	49.2393
15	0.7044	-0.0308	-0.9163	1.9082	-1.3038	2.575	0.1203	0.0086	0.3982	0.1134	0.1345	0.6595	-0.3701	-0.5493	-0.1582	0.1904	0.0302	-0.0606	0.1867	-0.0282	0.2026	31.5378	-7.9549	36.7198
16	0.4592	-0.2947	-0.0389	0.5326	-0.0945	1.3446	-0.0473	-0.1208	0.0128	-0.0639	-0.0214	-0.0875	0.1323	-0.1199	0.0422	0.1344	0.0162	0.0055	0.193	-0.0362	0.133	35.686	-17.2001	32.7128
17	0.4045	0.454	0.1056	1.6153	-0.4117	1.4318	0.003	0.0268	-0.0944	-0.0695	-0.0654	-0.1162	0.0515	0.1864	0.0797	0.1496	-0.0089	0.0057	0.2213	-0.0245	0.1306	43.7933	-19.495	31.3649
18	0.5188	-0.1952	-0.4589	1.487	-0.8053	2.4392	0.0268	-0.1369	-0.0375	0.0422	-0.1446	-0.2703	0.0834	0.3709	0.1488	0.141	-0.0166	-0.0345	0.2849	-0.0748	0.2411	50.1976	-12.2113	36.709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 201 through 227 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 228 through 246 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 11 through 25 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 26 through 43 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 44 through 67 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 68 through 108 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 109 through 125 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 126 through 200 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 201 through 247 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 11 through 25 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 26 through 43 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 44 through 67 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 68 through 88 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 89 through 108 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 109 through 125 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 126 through 146 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 147 through 177 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 178 through 200 )

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