PDB-8wbl: Crystal structure of cis-Epoxysuccinate Hydrolases RhCESH[L] comp...

ID or keywords:

Entry

Database: PDB / ID: 8wbl

Title

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

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: 1.941 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	8wbl.cif.gz	203.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbl.ent.gz	161.7 KB	Display	PDB format
PDBx/mmJSON format	8wbl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8wbkC 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

59.1 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)	43.530, 59.349, 64.571
Angle α, β, γ (deg.)	69.46, 73.64, 82.65
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.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.55 Å³/Da / Density % sol: 51.8 %
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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 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: 1.94→55.55 Å / Num. obs: 37230 / % possible obs: 86.7 % / Redundancy: 3.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.053 / R_pim(I) all: 0.032 / R_rim(I) all: 0.062 / Net I/σ(I): 12.9 / Num. measured all: 133999
Reflection shell	Resolution: 1.94→2.05 Å / % possible obs: 90.4 % / Redundancy: 3.6 % / R_merge(I) obs: 0.419 / Num. measured all: 20570 / Num. unique obs: 5677 / CC_1/2: 0.94 / R_pim(I) all: 0.256 / R_rim(I) all: 0.492 / Net I/σ(I) obs: 3.2

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
Aimless		data scaling
autoPROC		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.941→39.002 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2171	1801	4.86 %
R_work	0.1767	-	-
obs	0.1786	37081	86.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.941→39.002 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3722	0	20	115	3857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	3838
X-RAY DIFFRACTION	f_angle_d	1.53	5224
X-RAY DIFFRACTION	f_dihedral_angle_d	9.088	3114
X-RAY DIFFRACTION	f_chiral_restr	0.091	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 (%)
1.9411-1.9936	0.3628	149	0.3371	2863	X-RAY DIFFRACTION	91
1.9936-2.0523	0.3344	146	0.2733	2786	X-RAY DIFFRACTION	89
2.0523-2.1185	0.3999	130	0.32	2520	X-RAY DIFFRACTION	81
2.1185-2.1942	0.2616	163	0.2103	2672	X-RAY DIFFRACTION	85
2.1942-2.2821	0.2634	57	0.2095	1440	X-RAY DIFFRACTION	45
2.2821-2.3859	0.2214	128	0.1843	2937	X-RAY DIFFRACTION	93
2.3859-2.5117	0.2707	146	0.171	2897	X-RAY DIFFRACTION	93
2.5117-2.669	0.2249	137	0.1756	2920	X-RAY DIFFRACTION	92
2.669-2.875	0.2101	164	0.1675	2792	X-RAY DIFFRACTION	90
2.875-3.1642	0.2045	136	0.1744	2639	X-RAY DIFFRACTION	84
3.1642-3.6218	0.1901	158	0.1658	2992	X-RAY DIFFRACTION	95
3.6218-4.562	0.1825	145	0.1469	2953	X-RAY DIFFRACTION	94
4.562-39	0.1812	142	0.1549	2869	X-RAY DIFFRACTION	91

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	1.6938	0.4715	-0.987	3.4273	-1.0336	1.6241	0.1371	0.0306	0.3816	-0.1484	-0.0761	0.4999	-0.2156	-0.2495	-0.0267	0.4008	0.0467	-0.0194	0.3298	-0.0509	0.3782	-26.612	4.0678	-0.5947
2	0.8953	0.4648	-0.5329	0.3268	-0.0435	1.981	0.0313	-0.1606	-0.0374	-0.0408	-0.0342	0.0224	-0.0966	-0.0186	0.0216	0.2701	0.0652	-0.0214	0.2692	-0.0034	0.3019	-22.4254	-4.6368	-5.4876
3	1.109	1.0811	-0.388	2.0089	-0.8795	2.5491	0.0144	-0.2016	-0.1092	-0.1059	-0.1214	-0.299	-0.005	0.2778	0.0778	0.2858	0.048	0.001	0.3053	-0.0085	0.3541	-13.7129	-7.2149	-7.0846
4	2.0827	0.0432	-1.0234	2.2944	-0.4405	4.1918	0.1311	-0.2607	-0.1951	0.0674	-0.2547	-0.3231	0.0972	0.1908	0.0695	0.3214	-0.0641	-0.0346	0.4813	-0.0197	0.402	-7.6099	0.2919	-1.8271
5	4.3206	1.2416	-2.3135	1.7412	-0.3953	1.2394	0.7014	-1.4459	-0.1188	0.8481	-0.8043	-0.2333	-0.7907	1.1765	0.0843	0.5731	-0.1844	-0.0878	0.7194	-0.0286	0.3861	-13.4633	2.8641	11.0842
6	3.1159	0.429	0.3078	3.4611	-0.5546	4.137	-0.0642	-0.5869	0.7984	0.4109	-0.0798	0.3601	-0.8827	-0.3575	0.2304	0.5578	-0.0325	0.0232	0.3568	-0.098	0.5206	-18.2413	13.1043	0.5612
7	2.8515	0.7841	0.0238	1.1879	0.5681	1.8038	-0.1594	0.4589	0.2815	-0.19	0.1769	0.107	-0.2025	-0.1046	0.0144	0.3109	0.0279	-0.0172	0.2823	0.0265	0.3127	-23.7312	1.5573	-31.1035
8	2.8707	-0.3672	0.2883	6.5281	-0.7248	3.729	-0.2034	0.6888	-0.2468	-0.6224	0.0708	0.136	0.0997	0.0896	0.1165	0.3873	-0.0539	0.0474	0.5134	-0.073	0.3189	-16.8464	-4.8727	-39.282
9	2.2739	0.5532	0.0664	2.0001	-1.3416	3.0761	-0.1083	0.2132	-0.3096	0.0646	0.0531	-0.3775	-0.131	0.2829	0.0174	0.36	0.0199	0.0707	0.4148	-0.0486	0.4131	-9.1997	-5.7085	-34.0052
10	3.0127	1.5761	-0.5512	1.3843	-0.6177	1.2991	-0.1767	0.149	0.2946	-0.2546	0.1348	0.0457	-0.1555	0.0774	0.0148	0.3601	-0.019	-0.0078	0.34	0.0158	0.3276	-20.4288	3.9302	-29.7724
11	0.5002	-0.0792	0.3223	1.0171	0.1814	1.5422	-0.1451	-0.0145	0.002	-0.2945	0.1556	-0.0177	0.0214	0.0424	-0.0089	0.3067	0.0578	-0.0275	0.2577	-0.0121	0.3217	-23.716	-4.1874	-19.2631
12	1.7057	0.6029	-0.3769	0.5065	-0.9471	2.3638	-0.1175	-0.0152	-0.2584	-0.0788	0.0275	-0.1189	0.2639	0.078	0.0395	0.3024	0.0581	-0.0173	0.2669	0.0039	0.3672	-22.0356	-12.4926	-19.6105
13	1.5373	-0.4306	-0.1201	3.1555	-1.1313	3.4843	-0.1483	0.257	-0.4572	-0.2455	-0.1191	-0.2716	0.5847	0.0321	0.1365	0.4084	-0.0351	0.0113	0.3508	-0.0579	0.3985	-30.346	-17.6635	-24.4735
14	3.1642	1.8713	-0.6773	5.9882	-2.066	2.9346	-0.5048	0.8111	0.1202	-0.259	0.5759	-0.2446	0.0415	-0.8128	-0.0437	0.3079	0.0045	-0.0294	0.4095	-0.0061	0.3043	-33.2303	-6.365	-34.6755
15	1.4509	2.0575	-1.0508	5.3837	-3.8351	4.52	-0.3362	0.7248	0.3913	-0.7456	0.3601	-0.1832	0.027	0.1748	-0.2206	0.58	-0.0749	-0.0045	0.599	0.0368	0.4583	-37.1043	-13.7496	-36.979
16	1.9404	0.4497	-1.0921	2.0639	1.4997	2.6853	0.1054	0.3211	0.1443	-0.1936	-0.0748	0.3104	-0.2246	-0.3955	-0.001	0.286	0.0529	-0.0279	0.3819	-0.0048	0.3625	-42.6568	-5.9782	-22.75
17	1.0128	0.3187	0.3588	1.9601	-0.2097	1.843	0.1587	-0.365	0.0296	0.331	-0.1919	0.0882	-0.0889	0.0713	0.0367	0.3172	-0.0215	0.0025	0.3643	-0.0299	0.3083	-26.0416	-6.1646	6.8289
18	5.6333	0.1261	-1.1862	2.5229	-0.1083	2.8196	0.3501	-0.6168	-0.0697	0.5597	-0.5357	-0.4085	0.0436	0.21	0.0846	0.45	-0.0874	-0.0821	0.523	0.1173	0.393	-19.6937	-14.7156	12.9486
19	1.7681	0.5835	0.2982	1.4365	0.1552	1.7651	0.1311	-0.3299	-0.3728	0.084	-0.2441	-0.2033	0.4693	0.0644	0.1071	0.4419	-0.01	0.0014	0.4245	0.0776	0.4026	-24.9239	-21.4151	8.273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 109 through 125 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 126 through 147 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 148 through 177 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 178 through 200 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 201 through 227 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 228 through 247 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 11 through 43 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 44 through 68 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 69 through 88 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 89 through 125 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 126 through 146 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 147 through 177 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 178 through 200 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 201 through 217 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 218 through 227 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 228 through 247 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 11 through 43 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 44 through 67 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 68 through 108 )

-
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