PDB-7ac0: Epoxide hydrolase CorEH without ligand

ID or keywords:

Entry

Database: PDB / ID: 7ac0

Title

Epoxide hydrolase CorEH without ligand

Components

Soluble epoxide hydrolase

Keywords

HYDROLASE / epoxide hydrolase / dehalogenase

Function / homology

Function and homology information

soluble epoxide hydrolase / epoxide hydrolase activity / catabolic process / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Corynebacterium sp. C12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.177 Å

Authors

Palm, G.J. / Lammers, M. / Berndt, L.

Funding support

European Union, 1items

Citation

Journal: Acs Catalysis / Year: 2021
Title: Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12
Authors: Schuiten, E.D. / Badenhorst, C.P.S. / Palm, G.J. / Berndt, L. / Lammers, M. / Mican, J. / Bednar, D. / Damborsky, J. / Bornscheuer, U.T.

History

Deposition	Sep 9, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ac0.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb7ac0.ent.gz		Display	PDB format
PDBx/mmJSON format	7ac0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/7ac0 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/7ac0	HTTPS FTP

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Related structure data

Related structure data	3qyjS S: Starting model for refinement
Similar structure data	1h7o-1 1gjp-1 1w31-1 1h7n-1 1ylv-1 1h7r-1 2woq-1 1ohl-1 Search similar-shape structures by Omokage search (details) 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 (4) #165 - Sep 2013 Designed Protein Cages similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

AAA: Soluble epoxide hydrolase

BBB: Soluble epoxide hydrolase

CCC: Soluble epoxide hydrolase

DDD: Soluble epoxide hydrolase

EEE: Soluble epoxide hydrolase

FFF: Soluble epoxide hydrolase

GGG: Soluble epoxide hydrolase

HHH: Soluble epoxide hydrolase

273 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	140.016, 156.570, 112.581
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Soluble epoxide hydrolase / SEH / Cytosolic epoxide hydrolase / cEH / Epoxide hydratase Mass: 34171.613 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. C12 (bacteria) / Plasmid: pET28a / Details (production host): kanamycin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O52866, soluble epoxide hydrolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1112 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Soluble epoxide hydrolase / SEH / Cytosolic epoxide hydrolase / cEH / Epoxide hydratase

Mass: 34171.613 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Corynebacterium sp. C12 (bacteria) / Plasmid: pET28a / Details (production host): kanamycin resistance / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O52866, soluble epoxide hydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1112 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2 uL reservoir (16% PEG4000, 0.1 M Tris pH 9.5, 0.1 M NaOAc, 0.018 M imidazol pH 7.0) + 2 uL protein solution (10 mg/ml protein, 10 mM Tris pH 7.5, 20 mM NaCl) + 0.66 uL extra (1 M imidazol pH 6.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 20, 2020 / Details: mirrors
Radiation	Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.177→50 Å / Num. obs: 129462 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / B_iso Wilson estimate: 37.6 Å² / CC_1/2: 0.994 / R_rim(I) all: 0.22 / R_sym value: 0.203 / Net I/σ(I): 9.1
Reflection shell	Resolution: 2.177→2.31 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 20548 / CC_1/2: 0.547 / R_rim(I) all: 1.535 / R_sym value: 1.41 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	VERSION Mar 15, 2019	data reduction
XDS	VERSION Mar 15, 2019	data scaling
PHASER	Version: 2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QYJ

3qyj

Resolution: 2.177→47.394 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.188 / WR_factor R_work: 0.139 / SU B: 14.992 / SU ML: 0.184 / Average fsc free: 0.8822 / Average fsc work: 0.8987 / Cross valid method: FREE R-VALUE / ESU R: 0.249 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2262	6415	4.955 %	random selection
R_work	0.1734	123047	-	-
all	0.176	-	-	-
obs	-	129462	99.667 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 34.511 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.768 Å²	0 Å²	-0 Å²
2-	-	0.19 Å²	0 Å²
3-	-	-	0.578 Å²

Refinement step

Cycle: LAST / Resolution: 2.177→47.394 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18055	0	0	1112	19167

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	18700
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	17106
X-RAY DIFFRACTION	r_angle_refined_deg	1.759	1.637	25511
X-RAY DIFFRACTION	r_angle_other_deg	1.36	1.573	39335
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.304	5	2290
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.12	22.024	1018
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.343	15	2864
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.222	15	113
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	2343
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	21433
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4529
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	3991
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.177	0.2	16972
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	8801
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	8945
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	977
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.255	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.123	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.022	2.087	9098
X-RAY DIFFRACTION	r_mcbond_other	1.022	2.087	9097
X-RAY DIFFRACTION	r_mcangle_it	1.583	3.126	11366
X-RAY DIFFRACTION	r_mcangle_other	1.583	3.126	11367
X-RAY DIFFRACTION	r_scbond_it	1.149	2.194	9602
X-RAY DIFFRACTION	r_scbond_other	1.149	2.194	9602
X-RAY DIFFRACTION	r_scangle_it	1.837	3.251	14130
X-RAY DIFFRACTION	r_scangle_other	1.837	3.251	14130
X-RAY DIFFRACTION	r_lrange_it	4.003	24.661	21322
X-RAY DIFFRACTION	r_lrange_other	3.934	24.42	21126

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 (%)
2.177-2.233	0.342	476	0.303	8824	X-RAY DIFFRACTION	97.7918
2.233-2.295	0.322	467	0.283	8810	X-RAY DIFFRACTION	99.8923
2.295-2.361	0.315	431	0.268	8574	X-RAY DIFFRACTION	99.7011
2.361-2.434	0.268	419	0.242	8298	X-RAY DIFFRACTION	99.8854
2.434-2.513	0.286	415	0.23	8067	X-RAY DIFFRACTION	99.9646
2.513-2.602	0.29	423	0.219	7826	X-RAY DIFFRACTION	99.9152
2.602-2.7	0.252	395	0.197	7561	X-RAY DIFFRACTION	99.9749
2.7-2.81	0.243	399	0.182	7239	X-RAY DIFFRACTION	99.9738
2.81-2.935	0.28	373	0.189	6942	X-RAY DIFFRACTION	99.7137
2.935-3.078	0.224	306	0.182	6709	X-RAY DIFFRACTION	99.7299
3.078-3.245	0.245	321	0.179	6382	X-RAY DIFFRACTION	99.9851
3.245-3.441	0.225	317	0.17	6048	X-RAY DIFFRACTION	100
3.441-3.679	0.221	297	0.165	5677	X-RAY DIFFRACTION	99.9665
3.679-3.973	0.185	282	0.143	5311	X-RAY DIFFRACTION	99.875
3.973-4.352	0.183	244	0.126	4903	X-RAY DIFFRACTION	99.7674
4.352-4.866	0.166	228	0.116	4425	X-RAY DIFFRACTION	99.5933
4.866-5.617	0.176	233	0.116	3938	X-RAY DIFFRACTION	99.976
5.617-6.878	0.176	159	0.121	3365	X-RAY DIFFRACTION	99.9433
6.878-9.717	0.15	146	0.107	2624	X-RAY DIFFRACTION	99.2476
9.717-47	0.197	84	0.166	1526	X-RAY DIFFRACTION	98.2906

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	0.7789	0.402	-0.1069	1.1031	-0.0267	1.5045	-0.0194	0.0277	-0.0762	-0.1634	-0.0124	-0.0396	0.0748	0.088	0.0318	0.0324	0.0203	0.0048	0.0865	0.0103	0.0095	30.0836	19.1552	54.5507
2	1.2637	0.0302	-0.1068	1.3181	-0.1402	0.6743	-0.0104	-0.0643	-0.1902	-0.0732	-0.0242	-0.2449	0.0755	0.395	0.0346	0.0137	0.017	0.0075	0.4675	0.0714	0.0894	66.1827	23.3361	75.6766
3	0.7104	-0.0556	-0.386	1.2874	-0.3638	1.1395	0.0769	-0.0859	0.0978	0.0075	-0.0415	-0.0128	-0.0917	0.0819	-0.0355	0.0157	-0.0331	0.0119	0.1169	-0.0219	0.0149	44.7445	57.1533	60.605
4	1.3056	0.0892	-0.0336	0.7356	0.2276	1.1247	0.1181	-0.3687	0.1622	0.147	-0.1028	-0.0904	-0.1477	0.3053	-0.0154	0.1014	-0.1672	-0.0118	0.4936	-0.0441	0.0382	57.5973	55.3412	100.3426
5	1.3136	-0.0653	-0.069	1.4481	-0.1285	0.3596	0.1007	-0.2543	0.2708	0.0894	-0.0324	0.1335	-0.1311	0.0235	-0.0684	0.0761	-0.0555	0.0579	0.2112	-0.0911	0.0857	16.7643	63.0236	90.3345
6	0.9855	0.4183	-0.119	1.1792	-0.1215	1.6647	0.0945	-0.3887	0.0325	0.3849	-0.1011	0.1687	-0.0907	0.1487	0.0066	0.1667	-0.1049	0.0527	0.502	-0.0041	0.0262	27.3847	33.4544	118.1091
7	1.5932	0.4373	0.1551	0.4553	0.1989	0.8386	0.0128	-0.1534	0.004	0.0266	-0.0262	0.0588	0.0084	-0.0205	0.0134	0.0041	-0.0169	0.0028	0.1342	0.0114	0.0109	2.2153	25.038	84.2092
8	0.5638	-0.1061	-0.0324	1.1916	-0.0233	0.7674	-0.0419	-0.1479	-0.1567	0.1553	-0.0216	-0.0022	0.1874	0.1358	0.0634	0.0709	0.009	0.015	0.3347	0.1106	0.0611	35.9938	1.5791	93.4312

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	3 - 286
2	X-RAY DIFFRACTION	2	ALL	BBB	4 - 286
3	X-RAY DIFFRACTION	3	ALL	CCC	3 - 286
4	X-RAY DIFFRACTION	4	ALL	DDD	3 - 286
5	X-RAY DIFFRACTION	5	ALL	EEE	4 - 286
6	X-RAY DIFFRACTION	6	ALL	FFF	3 - 286
7	X-RAY DIFFRACTION	7	ALL	GGG	3 - 286
8	X-RAY DIFFRACTION	8	ALL	HHH	4 - 286

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