PDB-8wbs: Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L]-D48N...

ID or keywords:

Entry

Database: PDB / ID: 8wbs

Title

Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L]-D48N complexed with sulfate ions

Components

(S)-2-haloacid dehalogenase

Keywords

HYDROLASE / cis-Epoxysuccinate Hydrolases /

epoxide hydrolase / L(+)-tartaric acid

Function / homology

(S)-2-haloacid dehalogenase /

(S)-2-haloacid dehalogenase activity / L-2-Haloacid dehalogenase / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily /

metal ion binding /

(S)-2-haloacid dehalogenase

Function and homology information

Biological species

Klebsiella sp. BK-58 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 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

-
Download

PDBx/mmCIF format	8wbs.cif.gz	385.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbs.ent.gz	316.9 KB	Display	PDB format
PDBx/mmJSON format	8wbs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8wbkC 8wblC 8wbmC 8wbnC 8wboC 8wbpC 8wbqC 8wbrC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (4) #118 - Oct 2009 Sodium-Potassium Pump 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

110 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
55.2 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)	119.846, 94.426, 99.597
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-533- HOH

#1: Protein	(S)-2-haloacid dehalogenase / (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-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.14 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris, pH 6.5, 25% PEG 3350

-
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: Oct 27, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.03→119.85 Å / Num. obs: 73725 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.029 / R_rim(I) all: 0.108 / Χ²: 0.92 / Net I/σ(I): 14.9 / Num. measured all: 984724
Reflection shell	Resolution: 2.03→2.08 Å / % possible obs: 100 % / Redundancy: 12.2 % / R_merge(I) obs: 1.411 / Num. measured all: 65329 / Num. unique obs: 5375 / CC_1/2: 0.739 / R_pim(I) all: 0.42 / R_rim(I) all: 1.473 / Χ²: 0.94 / Net I/σ(I) obs: 2.2

-
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: 2.03→76.599 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2092	3813	5.18 %
R_work	0.1779	-	-
obs	0.1796	73616	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: 2.03→76.599 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7349	0	42	357	7748

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7551
X-RAY DIFFRACTION	f_angle_d	0.891	10242
X-RAY DIFFRACTION	f_dihedral_angle_d	4.884	4473
X-RAY DIFFRACTION	f_chiral_restr	0.054	1123
X-RAY DIFFRACTION	f_plane_restr	0.005	1300

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 (%)
2.03-2.0552	0.2797	137	0.2494	2534	X-RAY DIFFRACTION	99
2.0552-2.0823	0.2666	145	0.2325	2528	X-RAY DIFFRACTION	100
2.0823-2.1108	0.2822	169	0.2285	2556	X-RAY DIFFRACTION	100
2.1108-2.1409	0.275	130	0.2155	2560	X-RAY DIFFRACTION	100
2.1409-2.1729	0.268	152	0.2116	2529	X-RAY DIFFRACTION	100
2.1729-2.2069	0.2508	130	0.2031	2562	X-RAY DIFFRACTION	100
2.2069-2.243	0.1998	139	0.196	2555	X-RAY DIFFRACTION	100
2.243-2.2817	0.2254	148	0.1871	2560	X-RAY DIFFRACTION	100
2.2817-2.3232	0.2297	147	0.1849	2551	X-RAY DIFFRACTION	100
2.3232-2.3679	0.206	129	0.1773	2580	X-RAY DIFFRACTION	100
2.3679-2.4162	0.2143	141	0.1846	2544	X-RAY DIFFRACTION	100
2.4162-2.4688	0.1888	126	0.1815	2581	X-RAY DIFFRACTION	100
2.4688-2.5262	0.2385	139	0.1859	2568	X-RAY DIFFRACTION	100
2.5262-2.5894	0.2513	130	0.1906	2582	X-RAY DIFFRACTION	100
2.5894-2.6594	0.2549	129	0.1925	2574	X-RAY DIFFRACTION	100
2.6594-2.7377	0.2399	115	0.1949	2612	X-RAY DIFFRACTION	100
2.7377-2.826	0.1966	155	0.1846	2561	X-RAY DIFFRACTION	100
2.826-2.927	0.2136	139	0.1833	2594	X-RAY DIFFRACTION	100
2.927-3.0442	0.2077	136	0.1784	2586	X-RAY DIFFRACTION	100
3.0442-3.1828	0.2261	151	0.1805	2586	X-RAY DIFFRACTION	100
3.1828-3.3506	0.191	147	0.1809	2578	X-RAY DIFFRACTION	100
3.3506-3.5605	0.2389	137	0.177	2618	X-RAY DIFFRACTION	100
3.5605-3.8354	0.1968	161	0.1521	2591	X-RAY DIFFRACTION	100
3.8354-4.2214	0.1689	141	0.1528	2626	X-RAY DIFFRACTION	100
4.2214-4.8321	0.1663	140	0.1465	2633	X-RAY DIFFRACTION	100
4.8321-6.0876	0.2065	159	0.1832	2666	X-RAY DIFFRACTION	100
6.0876-76.59	0.2094	141	0.1892	2788	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	1.961	0.4851	1.5742	7.8119	3.8993	5.0346	0.2084	0.3779	-0.1047	-0.5022	-0.2497	0.1867	0.2389	0.0043	0.0466	0.2337	0.0841	0.0382	0.334	0.0222	0.2471	9.0434	22.2015	-7.0006
2	3.2651	1.4068	1.0553	4.8079	4.3238	9.6008	-0.0852	-0.1277	-0.0807	0.4261	-0.2883	0.7385	0.4206	-0.5381	0.2955	0.3342	0.0359	0.0726	0.2546	-0.0007	0.4711	5.9267	11.2882	3.1974
3	1.4543	-0.5372	0.2124	2.2382	0.192	1.4307	0.0728	0.1579	-0.1838	-0.2128	-0.1468	-0.0085	0.2053	0.1146	0.048	0.2078	0.0539	0.015	0.3054	-0.0351	0.2858	12.7907	21.7471	-5.4488
4	1.4293	0.1877	0.3177	1.4142	0.2024	1.0946	-0.0755	-0.1062	0.019	0.1735	0.0681	0.2272	0.0547	-0.1725	0.0085	0.22	0.0418	0.0458	0.2445	-0.0056	0.2942	5.6721	33.1459	6.4825
5	1.3959	0.4277	0.2372	6.9145	6.67	8.3145	0.1232	-0.1788	0.1107	-0.0335	0.1415	-0.3454	-0.5545	0.2297	-0.3283	0.2579	0.0013	0.0123	0.2512	0.0353	0.2359	35.5315	45.2207	18.1561
6	5.7421	3.8549	1.3827	6.8705	0.7462	1.8883	0.1995	-0.6247	-0.0747	0.9995	-0.2862	-0.3699	0.1008	0.1654	0.1251	0.4431	-0.004	-0.0608	0.3507	0.0118	0.2176	36.8602	40.3596	28.0367
7	6.891	-3.6961	-0.6491	2.6352	-1.2841	6.9277	-0.2778	-0.9471	0.1782	1.685	-0.1805	0.2346	-0.335	0.1047	0.2495	0.6472	-0.0806	0.0219	0.4085	0.0297	0.3882	27.0125	28.8475	31.6931
8	2.503	1.8041	2.143	9.2828	5.5848	7.0238	0.2424	-0.3034	0.2502	1.1345	-0.3902	0.3124	0.2643	-0.1815	0.0799	0.557	-0.045	0.0946	0.4056	0.0094	0.2961	29.4667	47.0009	30.3702
9	2.7676	0.1884	0.4004	2.0857	0.1739	2.1637	-0.0267	-0.0003	-0.1289	0.082	-0.0021	-0.0805	-0.0044	0.2973	0.0261	0.1869	0.0385	0.0024	0.1999	0.0155	0.1892	35.2813	30.006	11.3817
10	7.4263	-0.1982	-1.1973	3.1167	0.5811	2.1985	-0.2305	0.4803	0.1033	0.3627	0.0457	0.8816	-0.2062	-0.8447	0.1375	0.4032	0.1067	0.1056	0.6525	-0.0036	0.4952	20.6459	-6.496	23.1657
11	5.6645	2.3941	4.2013	1.4982	1.4836	4.3035	-0.5226	-0.5683	0.5107	-0.1936	0.2604	0.4569	-1.0893	-0.4485	0.1857	0.8326	0.1338	-0.1285	0.7143	0.0213	1.0455	23.0076	5.4579	27.1073
12	8.3559	0.3179	1.3784	3.9861	1.0721	4.9238	-0.4374	-1.2053	1.8796	0.522	0.1304	0.7756	-0.522	-0.7872	0.3832	0.7655	0.2302	0.1518	0.9458	-0.2104	1.055	17.2765	1.8093	34.2774
13	1.7951	0.0426	-0.912	3.4206	-0.8664	3.587	-0.0088	-0.179	0.2808	0.4754	0.0544	0.0528	-0.6205	-0.2955	-0.0333	0.3727	0.0578	-0.0086	0.3169	-0.0611	0.2978	37.2108	-6.3351	21.9574
14	7.8472	-4.6486	-2.1951	8.6033	1.4593	4.1464	-0.3493	-0.6603	0.4403	1.7499	0.3607	-0.401	-0.2702	0.3679	-0.0181	0.9405	0.0001	-0.0733	0.5518	-0.0411	0.3031	37.9451	-23.4704	44.1283
15	2.623	2.306	1.495	7.3606	1.1158	4.8643	0.08	-0.8008	0.1034	1.8406	-0.0694	-2.7062	-0.4141	0.4918	0.0696	1.2776	-0.0397	-0.6258	0.9792	0.007	1.3027	59.68	-20.7541	44.9833
16	2.2279	0.6328	-0.1598	2.1771	0.382	4.4059	0.2047	-0.2243	0.2341	1.1465	-0.2083	-0.0528	-0.3884	-0.1251	-0.0099	0.8814	0.015	-0.0444	0.4791	-0.0601	0.319	38.1256	-19.0376	41.9717
17	2.1596	1.2076	-0.5329	1.8246	1.8737	4.4328	0.316	-0.6512	-0.1487	1.3641	-0.2136	-0.1336	0.0975	0.1932	-0.0571	1.364	-0.061	-0.0552	0.6543	0.0074	0.4053	37.3228	-28.8188	52.9698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 42 through 76 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 119 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 120 through 157 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 158 through 274 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 42 through 76 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 77 through 92 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 93 through 104 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 105 through 139 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 140 through 274 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 42 through 76 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 77 through 96 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 97 through 139 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 140 through 274 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 42 through 55 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 56 through 139 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 140 through 221 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 222 through 274 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi