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

ID or keywords:

Entry

Database: PDB / ID: 8wbo

Title

Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] mutant D18N 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: 1.58 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
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8wbo.cif.gz	115.6 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	8wbkC 8wblC 8wbmC 8wbnC 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

hetero molecules

29.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Epoxide hydrolase

hetero molecules

A: Epoxide hydrolase

hetero molecules

defined by author
Evidence: gel filtration
59.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.804, 59.521, 68.677
Angle α, β, γ (deg.)	90.00, 108.41, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-471- HOH
2	1	A-604- HOH

#1: Protein	Epoxide hydrolase Mass: 29350.920 Da / Num. of mol.: 1 / Mutation: D18N 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris, pH 6.5, 26% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.58→50 Å / Num. obs: 33520 / % possible obs: 99.9 % / Redundancy: 6.7 % / R_merge(I) obs: 0.998 / Χ²: 0.019 / Net I/σ(I): 9 / Num. measured all: 225293

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
1.58-1.61	6.4	0.411	1679	0.925	1	99.9
1.61-1.64	6.8	0.364	1663	0.981	1	100
1.64-1.67	6.8	0.316	1647	0.949	1	100
1.67-1.7	6.7	0.292	1670	0.979	1	100
1.7-1.74	6.8	0.24	1676	0.962	1	100
1.74-1.78	6.6	0.204	1645	0.969	1	100
1.78-1.82	6.2	0.167	1724	1.02	1	99.9
1.82-1.87	6.9	0.144	1632	1.021	1	100
1.87-1.93	6.9	0.124	1670	1.014	1	99.9
1.93-1.99	6.9	0.099	1711	0.996	1	100
1.99-2.06	6.7	0.084	1662	0.964	1	100
2.06-2.14	6.5	0.067	1666	0.947	1	99.9
2.14-2.24	6.4	0.06	1649	0.961	1	99.7
2.24-2.36	7	0.055	1691	0.962	1	100
2.36-2.51	7	0.05	1688	0.935	1	100
2.51-2.7	6.8	0.045	1675	0.908	1	99.9
2.7-2.97	6.5	0.039	1672	0.874	1	99.5
2.97-3.4	7.1	0.035	1688	0.837	1	99.9
3.4-4.29	6.5	0.03	1698	0.82	1	99.2
4.29-50	6.8	0.031	1714	0.854	1	99.2

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Processing

Software

Name	Version	Classification
HKL-3000		data scaling
PHENIX	1.2	refinement
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.58→30.27 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1782	1675	5.01 %
R_work	0.1502	-	-
obs	0.1516	33466	99.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.58→30.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1861	0	10	251	2122

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1922
X-RAY DIFFRACTION	f_angle_d	0.988	2615
X-RAY DIFFRACTION	f_dihedral_angle_d	12.259	268
X-RAY DIFFRACTION	f_chiral_restr	0.054	290
X-RAY DIFFRACTION	f_plane_restr	0.009	338

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 (%)
1.58-1.62	0.2315	133	0.1783	2578	X-RAY DIFFRACTION	98
1.62-1.68	0.1944	126	0.1596	2691	X-RAY DIFFRACTION	100
1.68-1.74	0.1934	139	0.1529	2587	X-RAY DIFFRACTION	100
1.74-1.81	0.1705	147	0.1554	2678	X-RAY DIFFRACTION	100
1.81-1.89	0.1865	141	0.1547	2636	X-RAY DIFFRACTION	100
1.89-1.99	0.1696	144	0.1459	2643	X-RAY DIFFRACTION	100
1.99-2.11	0.1793	118	0.1435	2654	X-RAY DIFFRACTION	100
2.11-2.28	0.189	173	0.1455	2636	X-RAY DIFFRACTION	100
2.28-2.5	0.1754	130	0.1492	2658	X-RAY DIFFRACTION	100
2.51-2.87	0.2054	147	0.1619	2656	X-RAY DIFFRACTION	100
2.87-3.61	0.1725	153	0.1487	2659	X-RAY DIFFRACTION	100
3.61-30.27	0.1505	124	0.1425	2715	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	2.6979	0.2867	1.53	1.1757	0.2307	2.2194	0.0744	-0.4517	-0.0806	0.2343	-0.0664	-0.0651	0.0758	-0.0939	-0.0225	0.1082	-0.0342	-0.0006	0.1274	0.0332	0.072	-20.305	28.1503	84.7819
2	2.072	0.4495	0.7214	3.2219	-1.3918	3.8695	0.0569	-1.0689	0.2202	0.3991	0.0366	0.4466	-0.249	-0.2293	0.0139	0.1521	-0.063	0.0313	0.3604	-0.0616	0.0228	-20.6131	37.944	91.8609
3	1.4568	0.1514	1.1682	1.223	-0.3942	3.7539	-0.0911	-0.41	0.2261	0.092	0.0396	-0.0876	-0.2603	0.1885	0.044	0.1131	-0.0364	-0.0159	0.2086	-0.0364	0.111	-11.8334	40.0058	88.5395
4	3.1072	1.5737	1.8049	3.2052	0.7751	4.1605	0.2028	-0.0643	-0.3219	0.1417	-0.0831	-0.1033	0.2562	0.1232	-0.1138	0.0624	-0.0149	0.0235	0.0497	0.0179	0.116	-26.1021	21.2503	75.1217
5	0.9355	0.0291	0.3325	1.1801	0.1097	1.6088	-0.0366	-0.1777	0.0044	0.0472	0.0009	0.0464	-0.0359	-0.0166	0.041	0.0505	-0.0099	0.0162	0.0421	0.0002	0.0562	-22.715	30.7752	72.0719
6	1.5696	1.1672	0.2683	1.4898	0.1695	3.1322	0.0039	-0.0252	0.244	-0.0033	-0.0655	0.0996	-0.2413	-0.1618	0.0381	0.0579	0.0053	-0.0036	0.0582	-0.0054	0.0787	-27.4138	38.644	70.6357
7	1.885	-0.8148	1.06	2.7021	-1.4811	5.4095	-0.0071	-0.2246	0.2484	0.122	-0.0196	0.1484	-0.2529	-0.178	0.0282	0.0738	0.0024	0.0315	0.0957	-0.0364	0.167	-37.4588	36.6193	74.6859
8	2.3209	-0.0894	1.1963	1.4317	-0.6705	1.5733	0.1047	-1.1705	0.1389	0.6136	-0.3449	0.3449	-0.1901	-0.375	-0.2712	0.235	-0.123	0.1316	0.4512	-0.0052	0.0986	-36.2778	29.2038	86.9559
9	2.3974	-0.5385	-0.1486	0.9975	1.6581	3.9861	0.1791	-0.2809	-0.3923	0.2613	-0.1025	0.2399	0.2685	-0.1767	0.0004	0.1207	-0.062	0.0223	0.0888	0.0185	0.1806	-38.298	19.7789	75.0302

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 108 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 109 through 125 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 126 through 147 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 148 through 177 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 178 through 200 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 201 through 227 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 228 through 247 )

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