PDB-8wbt: Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L] muta...

ID or keywords:

Entry

Database: PDB / ID: 8wbt

Title

Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L] mutant D48N complexed with L-TA

Components

(S)-2-haloacid dehalogenase

Keywords

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

Function / homology

Function and homology information

hydrolase activity, acting on acid halide bonds, in C-halide compounds / metal ion binding
Similarity search - Function

Biological species

Klebsiella sp. BK-58 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 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	8wbt.cif.gz	399.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbt.ent.gz	327.8 KB	Display	PDB format
PDBx/mmJSON format	8wbt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wbt_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8wbt_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8wbt_validation.xml.gz	42.2 KB	Display
Data in CIF	8wbt_validation.cif.gz	60.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/8wbt ftp://data.pdbj.org/pub/pdb/validation_reports/wb/8wbt	HTTPS FTP

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Related structure data

Related structure data	8wbkC 8wblC 8wbmC 8wbnC 8wboC 8wbpC 8wbqC 8wbrC 8wbsC 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) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: (S)-2-haloacid dehalogenase

B: (S)-2-haloacid dehalogenase

C: (S)-2-haloacid dehalogenase

D: (S)-2-haloacid dehalogenase

hetero molecules

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: (S)-2-haloacid dehalogenase

B: (S)-2-haloacid dehalogenase

hetero molecules

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

2

C: (S)-2-haloacid dehalogenase

D: (S)-2-haloacid dehalogenase

hetero molecules

defined by author&software
55.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.620, 93.150, 101.640
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-405- HOH

#1: Protein	(S)-2-haloacid dehalogenase Mass: 27410.104 Da / Num. of mol.: 4 / Mutation: D48N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella sp. BK-58 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8PFD2
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.58 Å³/Da / Density % sol: 52.37 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium tartrate dibasic, pH7.0, 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: BL17U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 4, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.05→30.29 Å / Num. obs: 71832 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.126 / R_pim(I) all: 0.053 / R_rim(I) all: 0.137 / Χ²: 0.98 / Net I/σ(I): 11.4 / Num. measured all: 476882
Reflection shell	Resolution: 2.05→2.1 Å / % possible obs: 99.6 % / Redundancy: 6.4 % / R_merge(I) obs: 0.954 / Num. measured all: 33476 / Num. unique obs: 5212 / CC_1/2: 0.714 / R_pim(I) all: 0.404 / R_rim(I) all: 1.038 / Χ²: 0.96 / Net I/σ(I) obs: 2.1

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Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	v1.21	refinement
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.05→30.29 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2071	3635	5.07 %
R_work	0.1684	-	-
obs	0.1703	71767	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.05→30.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7452	0	72	604	8128

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7702
X-RAY DIFFRACTION	f_angle_d	0.841	10440
X-RAY DIFFRACTION	f_dihedral_angle_d	5.357	4991
X-RAY DIFFRACTION	f_chiral_restr	0.05	1143
X-RAY DIFFRACTION	f_plane_restr	0.005	1337

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 (%)
2.05-2.077	0.2659	159	0.2327	2562	X-RAY DIFFRACTION	99
2.077-2.1054	0.2782	144	0.2231	2556	X-RAY DIFFRACTION	100
2.1054-2.1355	0.2542	131	0.2117	2582	X-RAY DIFFRACTION	100
2.1355-2.1674	0.2856	140	0.2097	2635	X-RAY DIFFRACTION	100
2.1674-2.2012	0.246	152	0.2096	2542	X-RAY DIFFRACTION	100
2.2012-2.2373	0.2244	132	0.2021	2592	X-RAY DIFFRACTION	100
2.2373-2.2759	0.2501	141	0.1998	2613	X-RAY DIFFRACTION	100
2.2759-2.3172	0.2305	158	0.19	2573	X-RAY DIFFRACTION	100
2.3172-2.3618	0.2305	138	0.1819	2589	X-RAY DIFFRACTION	100
2.3618-2.41	0.2232	146	0.1867	2596	X-RAY DIFFRACTION	100
2.41-2.4623	0.2387	137	0.1855	2619	X-RAY DIFFRACTION	100
2.4623-2.5196	0.2144	154	0.1796	2577	X-RAY DIFFRACTION	100
2.5196-2.5826	0.2312	120	0.176	2597	X-RAY DIFFRACTION	100
2.5826-2.6524	0.2303	138	0.1676	2636	X-RAY DIFFRACTION	100
2.6524-2.7304	0.2264	126	0.1746	2621	X-RAY DIFFRACTION	100
2.7304-2.8184	0.2217	136	0.1681	2606	X-RAY DIFFRACTION	100
2.8184-2.9191	0.2104	152	0.1704	2609	X-RAY DIFFRACTION	100
2.9191-3.0359	0.2065	124	0.1609	2623	X-RAY DIFFRACTION	100
3.0359-3.1739	0.1898	162	0.157	2607	X-RAY DIFFRACTION	100
3.1739-3.341	0.1923	151	0.1648	2633	X-RAY DIFFRACTION	100
3.341-3.55	0.1996	120	0.1593	2627	X-RAY DIFFRACTION	100
3.55-3.8237	0.1711	125	0.152	2663	X-RAY DIFFRACTION	100
3.8237-4.2075	0.1778	125	0.1441	2685	X-RAY DIFFRACTION	100
4.2075-4.8143	0.1666	136	0.1331	2676	X-RAY DIFFRACTION	100
4.8143-6.0575	0.2063	146	0.1731	2705	X-RAY DIFFRACTION	100
6.0575-30.29	0.204	142	0.1721	2808	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	6.2623	0.7181	0.9244	4.6578	1.4864	5.7342	0.0332	-0.2953	-0.004	0.476	-0.2489	0.111	0.1604	-0.2132	0.2135	0.1112	0.0325	0.022	0.1064	0.039	0.1308	8.439	34.823	5.515
2	7.9568	-4.6566	-5.4995	7.3985	5.2813	8.358	0.193	0.2711	-0.4381	-1.0779	-0.2964	-0.0507	-0.1608	-0.2431	0.1648	0.3094	0.0165	-0.0246	0.2052	0.0372	0.253	8.508	14.072	-14.657
3	4.6935	2.4402	2.7368	7.6679	1.5748	3.0135	0.052	-0.5187	0.2283	0.5774	-0.3776	0.8055	-0.2148	-1.6783	0.2134	0.245	-0.0171	0.0559	0.3674	-0.0474	0.4215	2.58	12.629	0.673
4	0.8876	-0.1904	-0.4012	3.7749	2.7394	2.1193	0.0987	-0.2946	-0.1235	1.1808	-0.2868	0.1927	1.0673	-0.392	0.1716	0.4893	-0.0433	0.0418	0.2969	0.0319	0.3539	8.638	8.774	5.05
5	0.6236	-0.0319	0.0526	1.5578	0.3049	0.779	-0.0191	-0.0092	-0.0478	0.0595	0.0413	0.0396	0.1075	0.0003	-0.014	0.1667	0.009	0.0041	0.1741	0.0065	0.2041	12.98	25.475	2.671
6	2.4684	0.5714	1.2286	1.8612	2.352	5.924	-0.0486	-0.1785	0.0798	0.1367	-0.0423	0.2052	0.0703	-0.261	0.1055	0.1315	0.0084	0.04	0.133	0.0197	0.1853	-1.025	33.508	5.637
7	1.6169	-2.0329	0.7085	5.009	0.422	4.135	-0.0075	0.0707	0.0668	-0.3535	-0.1564	-0.1241	-0.3231	-0.0569	0.1008	0.1279	0.005	0.0168	0.1778	0.017	0.1934	4.625	42.301	0.222
8	2.8906	2.5251	1.9491	4.6777	2.2709	2.5404	-0.0212	0.0788	0.0053	-0.0751	0.0427	0.0528	-0.0564	0.136	0.0216	0.1665	0.0138	-0.0072	0.1835	0.0279	0.171	33.849	30.134	9.736
9	6.1307	-2.685	-2.5242	3.8052	4.5813	5.6823	0.2668	-0.693	0.677	-0.1519	-0.0763	-0.3632	-1.4316	0.145	-0.106	0.6107	-0.0389	-0.0163	0.3614	-0.0537	0.4113	35.609	53.599	23.446
10	7.2066	5.3489	-3.0656	4.6565	-4.0002	5.1362	-0.1441	-0.7931	-0.3748	0.6026	-0.4548	-1.0098	0.0807	0.2508	0.568	0.6248	0.0028	-0.1026	0.4598	0.0127	0.3548	35.033	38.631	30.083
11	2.3808	1.7621	-0.2886	7.0493	-0.5842	0.5593	0.1995	-0.6998	0.0751	1.1421	-0.4266	0.167	0.3329	-0.2212	0.24	0.7718	-0.0474	0.0511	0.5023	-0.0748	0.2799	26.85	37.662	32.272
12	5.4234	1.9711	2.0011	4.5196	3.7008	5.9749	0.1317	-0.42	1.1049	0.8348	-0.6043	0.4776	-0.4891	-0.3137	0.4286	0.6132	-0.0522	0.0239	0.2568	-0.0576	0.4884	28.515	50.395	28.997
13	2.3232	0.7346	-0.0177	1.6902	-0.1104	2.0875	-0.0488	-0.0309	0.0095	0.0532	-0.0203	-0.0265	-0.0799	-0.041	0.0597	0.1223	0.0319	-0.0052	0.1203	0.0051	0.1555	28.236	31.169	11.242
14	3.9252	1.8747	0.4891	5.7883	0.9254	1.9051	-0.0148	-0.0789	-0.2507	0.2353	0.098	-0.3498	-0.016	0.1252	-0.0965	0.128	0.0402	-0.0141	0.1755	0.0184	0.1879	39.389	26.238	13.739
15	2.5676	-3.1853	-2.3429	8.0582	1.8109	3.696	-0.0833	0.0102	0.1872	0.3595	0.1215	-0.3232	0.0058	0.3513	-0.0343	0.1748	-0.0124	-0.0062	0.2382	0.0384	0.3044	47.862	27.171	12.196
16	6.7815	-0.5484	-2.6881	8.7804	3.8892	2.6558	0.0112	0.6382	0.0485	-0.4563	-0.0244	-0.4133	-0.0309	0.8437	0.0963	0.2325	-0.0065	0.0505	0.2776	-0.0045	0.1962	41.17	30.145	-0.565
17	3.0978	0.7904	3.8786	3.9164	-1.3481	6.4335	0.1643	0.3246	0.4546	-0.0443	-0.1234	-0.2183	-0.0931	-0.1686	-0.0717	0.2384	0.0082	0.0517	0.2438	-0.0487	0.1991	37.465	-8.018	22.437
18	5.9439	5.654	-4.8132	8.7356	-3.5233	5.2939	0.0337	0.0559	-0.3492	0.2547	0.1794	0.6309	-0.1494	-0.4149	-0.1825	0.284	0.1103	-0.0044	0.5362	-0.0217	0.3663	10.757	-4.436	23.998
19	5.6313	5.4708	7.0002	7.2206	5.8461	8.9592	-0.4462	0.5433	0.6437	0.017	0.4672	-0.3627	-0.7475	0.549	-0.0559	0.4216	0.0914	0.0016	0.5321	-0.0654	0.5698	22.535	7.215	28.522
20	8.4744	-0.6509	3.9206	2.7684	1.6402	7.3481	-0.7967	-1.3928	1.0489	0.385	0.4508	-0.1093	-0.2709	-0.1572	0.3409	0.4592	0.1788	0.043	0.6947	-0.2229	0.5174	22.052	5.776	36.715
21	2.9849	-0.702	0.0804	2.0403	0.8115	1.5626	-0.4198	-0.8249	0.0111	0.3836	0.2236	0.5514	-0.0116	-0.1273	0.2043	0.3202	0.1253	0.0699	0.5629	-0.0041	0.3942	14.348	-3.075	31.224
22	1.9821	-0.1561	-0.3763	2.6091	-0.0026	3.4987	-0.0498	-0.3757	0.1651	0.2255	0.1158	0.0224	-0.2399	-0.0231	-0.0598	0.2158	0.0356	0.0079	0.2621	-0.0269	0.1732	38.999	-8.197	27.679
23	8.331	1.8415	1.8739	3.2516	-0.5081	4.9671	-0.235	0.0084	0.7022	-0.1965	0.1027	0.1095	-0.6384	-0.3002	0.1703	0.3306	0.0583	0.0289	0.171	-0.0577	0.2487	36.729	1.271	14.944
24	7.6684	-4.5201	-0.0428	2.8292	-0.5583	3.0046	-0.0777	-0.0961	-0.2147	-0.3924	-0.0732	0.2757	0.0746	-0.1588	0.1229	0.2061	-0.0129	0.0121	0.2049	-0.0383	0.1588	40.135	-13.429	11.855
25	8.397	-2.6507	0.0666	6.2968	0.6216	4.4236	0.1365	-0.1353	-0.177	0.2954	0.0225	-1.3355	0.5361	1.1535	-0.1957	0.5977	0.1208	-0.0496	0.6843	0.0802	0.5069	52.64	-27.73	41.567
26	7.6426	-3.2549	0.4954	7.0657	0.0437	7.3764	0.0134	-1.0717	0.6153	1.4566	0.0234	-1.3171	-0.4591	1.4648	-0.1417	0.9236	-0.2149	-0.2751	1.1815	0.0272	0.7434	59.683	-16.064	48.74
27	3.6403	-2.0996	1.3031	4.1495	2.0467	3.1622	0.2123	0.4725	0.6119	-0.0897	-0.6125	-2.5098	0.0716	2.2669	-0.0444	0.5954	0.2365	-0.0188	1.4897	0.3846	1.3432	65.693	-22.033	38.852
28	2.0583	0.5164	-0.2313	2.5361	-1.0454	3.8105	0.0414	-0.5671	-0.1325	0.6072	-0.0878	0.0032	0.1001	0.0859	0.0296	0.4693	0.0304	0.0234	0.4713	0.0194	0.2048	38.022	-22.04	46.627

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 40:55 )	A	40 - 55
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 56:76 )	A	56 - 76
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 77:96 )	A	77 - 96
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 97:119 )	A	97 - 119
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 120:208 )	A	120 - 208
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 209:258 )	A	209 - 258
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 259:276 )	A	259 - 276
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 41:55 )	B	41 - 55
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 56:76 )	B	56 - 76
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 77:96 )	B	77 - 96
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 97:119 )	B	97 - 119
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 120:139 )	B	120 - 139
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 140:208 )	B	140 - 208
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 209:248 )	B	209 - 248
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 249:264 )	B	249 - 264
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 265:275 )	B	265 - 275
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 41:55 )	C	41 - 55
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 56:76 )	C	56 - 76
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 77:97 )	C	77 - 97
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 98:119 )	C	98 - 119
21	X-RAY DIFFRACTION	21	( CHAIN C AND RESID 120:144 )	C	120 - 144
22	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 145:221 )	C	145 - 221
23	X-RAY DIFFRACTION	23	( CHAIN C AND RESID 222:258 )	C	222 - 258
24	X-RAY DIFFRACTION	24	( CHAIN C AND RESID 259:277 )	C	259 - 277
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 41:76 )	D	41 - 76
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 77:119 )	D	77 - 119
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 120:139 )	D	120 - 139
28	X-RAY DIFFRACTION	28	( CHAIN D AND RESID 140:275 )	D	140 - 275

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