PDB-8wbk: Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L]

ID or keywords:

Entry

Database: PDB / ID: 8wbk

Title

Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L]

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: 2.15 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	8wbk.cif.gz	205 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbk.ent.gz	163.2 KB	Display	PDB format
PDBx/mmJSON format	8wbk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8wblC 8wbmC 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

-
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)	42.130, 55.620, 64.200
Angle α, β, γ (deg.)	67.34, 75.80, 75.80
Int Tables number	1
Space group name H-M	P1

#1: Protein	Epoxide hydrolase / Mass: 29351.908 Da / Num. of mol.: 2 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 / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.26 Å³/Da / Density % sol: 45.57 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium sulfate

-
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: Apr 3, 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: 2.15→58.4 Å / Num. obs: 26753 / % possible obs: 95.5 % / Redundancy: 2 % / CC_1/2: 0.993 / R_merge(I) obs: 0.051 / R_pim(I) all: 0.051 / R_rim(I) all: 0.072 / Net I/σ(I): 8.5 / Num. measured all: 52583
Reflection shell	Resolution: 2.15→2.21 Å / % possible obs: 96.7 % / Redundancy: 2 % / R_merge(I) obs: 0.165 / Num. measured all: 3972 / Num. unique obs: 2005 / CC_1/2: 0.964 / R_pim(I) all: 0.165 / R_rim(I) all: 0.233 / Net I/σ(I) obs: 3.1

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→34.46 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2578	1999	7.49 %
R_work	0.2052	-	-
obs	0.2092	26685	95.32 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.15→34.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3722	0	5	154	3881

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3826
X-RAY DIFFRACTION	f_angle_d	1.845	5206
X-RAY DIFFRACTION	f_dihedral_angle_d	9.736	534
X-RAY DIFFRACTION	f_chiral_restr	0.136	582
X-RAY DIFFRACTION	f_plane_restr	0.01	674

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 (%)
2.15-2.2	0.3285	145	0.2483	1792	X-RAY DIFFRACTION	97
2.2-2.26	0.4377	141	0.3843	1747	X-RAY DIFFRACTION	95
2.26-2.33	0.3917	141	0.331	1728	X-RAY DIFFRACTION	93
2.33-2.4	0.2557	144	0.2191	1782	X-RAY DIFFRACTION	97
2.4-2.49	0.2454	146	0.2151	1801	X-RAY DIFFRACTION	97
2.49-2.59	0.3185	143	0.2219	1766	X-RAY DIFFRACTION	95
2.59-2.71	0.2943	142	0.212	1751	X-RAY DIFFRACTION	96
2.71-2.85	0.2444	145	0.2132	1794	X-RAY DIFFRACTION	97
2.85-3.03	0.2565	147	0.2135	1809	X-RAY DIFFRACTION	96
3.03-3.26	0.2887	144	0.2036	1783	X-RAY DIFFRACTION	97
3.26-3.59	0.2645	145	0.1939	1784	X-RAY DIFFRACTION	97
3.59-4.11	0.2261	145	0.1697	1789	X-RAY DIFFRACTION	97
4.11-5.17	0.1925	146	0.1573	1806	X-RAY DIFFRACTION	97
5.17-34.46	0.2209	125	0.1922	1554	X-RAY DIFFRACTION	84

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	1.3644	-0.1317	0.433	4.0478	-0.2896	1.9223	-0.1965	0.5051	0.1526	0.0091	0.2748	0.2096	0.047	-0.325	0.0318	0.1557	-0.0421	-0.005	0.3275	0.0065	0.2651	-24.8497	-11.3942	-20.8827
2	3.4434	0.5926	0.3802	1.8012	-0.0039	2.0376	-0.173	0.1288	1.0091	-0.0595	0.2232	0.3187	-0.2711	-0.0154	0.0021	0.2948	-0.0289	-0.0411	0.4769	0.1392	0.4024	-10.0461	4.8052	-37.3014
3	2.4395	-0.364	-1.3639	6.3814	-1.8085	2.8778	-0.2527	0.3839	-0.5471	-0.5632	0.5261	1.1191	0.4446	-0.1867	-0.1668	0.3022	0.0413	-0.0097	0.3683	-0.0077	0.3818	-9.8872	-10.3768	-36.7249
4	2.271	0.0948	-1.2816	2.2335	-1.9266	3.9632	-0.3852	-0.3538	-0.532	-0.2199	-0.165	-0.6982	0.4622	0.4957	0.366	0.2923	0.0976	0.0798	0.4299	0.0538	0.3197	-2.7626	-10.8294	-31.0108
5	2.6537	1.6053	-1.2953	0.9116	-0.831	0.8871	0.0666	-0.068	0.4581	0.0064	-0.0174	0.1289	-0.2069	0.2242	0.0165	0.3018	0.0291	-0.038	0.3985	0.0602	0.3245	-13.5703	-0.2438	-28.307
6	2.6662	0.0112	0.4594	1.4096	-0.4571	3.2433	0.0977	-0.0218	-0.1907	-0.0679	-0.1253	-0.1008	0.3116	0.0046	0.0262	0.1699	0.0159	0.011	0.1721	0.0167	0.1694	-19.7764	-15.184	-18.6023
7	1.5068	0.6969	0.0491	4.3442	-1.8973	1.7418	-0.2047	0.4663	0.0253	-0.4109	0.11	0.0334	0.0778	-0.4183	0.1305	0.2696	-0.0416	0.0004	0.4923	0.024	0.186	-26.7107	-9.7409	-32.8836
8	3.3796	0.5949	0.7296	4.9506	-0.394	3.0374	-0.1104	0.3799	0.2502	-0.5633	-0.2144	0.3362	-0.1228	-0.4754	0.2893	0.2678	-0.0144	-0.0614	0.4414	-0.0411	0.2935	-34.8897	-11.1852	-26.524
9	1.9696	-0.5303	0.745	2.7249	0.3077	0.9924	0.3682	-0.7345	0.0468	0.7335	-0.6651	-0.4995	-0.5219	0.7988	0.099	0.3332	-0.0862	-0.083	0.2854	-0.0043	0.3149	-12.0058	-1.5577	0.1419
10	2.2988	0.7611	-0.3529	4.3821	-0.7555	3.7577	0.0491	-0.0599	0.4082	0.3473	0.3194	0.8168	-0.7124	-0.4928	-0.2928	0.3714	0.0386	0.0331	0.3927	-0.0175	0.2647	-30.907	-13.353	15.6298
11	3.3559	0.0569	-0.4605	2.1797	-0.8137	2.1329	0.2878	-1.0831	0.131	0.3311	-0.4297	-0.1726	-0.3464	0.5306	0.1761	0.3979	-0.1234	-0.0434	0.5468	0.0471	0.3164	-16.7871	-16.3039	15.745
12	1.3831	0.8764	-1.0961	1.218	-0.8914	1.9986	-0.027	-0.2828	-0.2515	-0.1986	-0.2767	-0.3957	0.2603	0.5491	0.3974	0.3063	0.0102	0.0362	0.419	0.0988	0.3526	-16.4374	-23.7406	9.2591
13	1.9683	-0.4225	-0.5701	2.6194	-0.8429	3.0909	-0.0722	-0.0869	-0.2146	0.0261	0.184	0.0407	0.056	-0.5544	-0.0717	0.2503	-0.0126	0.0141	0.3407	0.0124	0.2742	-28.8008	-22.131	12.9095
14	2.0267	0.5566	-0.5305	2.6653	-0.7348	2.6735	-0.1652	0.1926	0.615	-0.1704	0.3451	0.5213	-0.6433	-0.6582	0.0436	0.5194	0.0168	-0.0754	0.2696	-0.0629	0.3387	-21.4169	1.9399	0.7643
15	1.6656	0.1229	-0.0915	1.6135	-0.9149	1.8068	-0.0876	0.0206	0.0859	0.0221	-0.0818	-0.1261	-0.178	0.0961	0.1121	0.2751	-0.0377	-0.0118	0.2569	0.0016	0.1906	-16.7801	-7.8083	-4.3385
16	0.6647	0.1911	0.7091	2.6786	-1.4724	3.3893	0.1983	-0.2516	0.0804	0.1728	-0.6956	-0.6947	-0.3698	1.1151	0.3012	0.273	-0.1155	-0.0387	0.4629	0.0949	0.399	-4.0053	-7.3635	-2.8074
17	1.5573	-0.0024	-0.8362	1.3086	0.745	3.7375	0.0347	-0.4312	-0.0753	0.7128	-0.3347	-0.7527	-0.6388	1.1226	0.1658	0.652	-0.1795	-0.1506	0.5164	-0.0096	0.4789	-6.3102	-2.1739	7.776
18	4.3026	0.5997	0.5396	1.971	-1.3325	1.2288	0.3325	-1.8894	0.3196	1.4445	-0.2488	0.1568	-0.5143	-0.5013	-0.0209	1.26	-0.5494	-0.3378	1.1614	-0.0071	0.6268	-7.2836	1.4735	15.3346
19	4.2917	0.9509	0.4288	1.571	-0.5418	4.6983	0.362	-0.8387	1.5629	0.6762	-0.1417	0.1758	-1.6302	-0.315	-0.0656	0.9011	-0.0938	-0.0082	0.361	-0.0565	0.6888	-13.3209	10.884	1.8464

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 43 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 44 through 68 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 88 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 89 through 125 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 126 through 200 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 201 through 217 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 218 through 247 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 11 through 25 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 26 through 43 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 44 through 67 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 68 through 88 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 89 through 108 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 109 through 125 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 126 through 160 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 161 through 190 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 191 through 213 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 214 through 228 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 229 through 247 )

-
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