PDB-8wbr: Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L]

ID or keywords:

Entry

Database: PDB / ID: 8wbr

Title

Crystal structure of cis-Epoxysuccinate Hydrolases KlCESH[L]

Components

(S)-2-haloacid dehalogenase

Keywords

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

Function / homology

hydrolase activity, acting on halide bonds, in C-halide compounds / L-2-Haloacid dehalogenase / : / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / metal ion binding / Cis-epoxysuccinate hydrolase

Function and homology information

Biological species

Klebsiella sp. BK-58 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.02 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	8wbr.cif.gz	206.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8wbr.ent.gz	163.9 KB	Display	PDB format
PDBx/mmJSON format	8wbr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8wbr_validation.pdf.gz	437.3 KB	Display	wwPDB validaton report
Full document	8wbr_full_validation.pdf.gz	441.8 KB	Display
Data in XML	8wbr_validation.xml.gz	20.6 KB	Display
Data in CIF	8wbr_validation.cif.gz	29.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wb/8wbr ftp://data.pdbj.org/pub/pdb/validation_reports/wb/8wbr	HTTPS FTP

-
Related structure data

Related structure data	8wbkC 8wblC 8wbmC 8wbnC 8wboC 8wbpC 8wbqC 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: (S)-2-haloacid dehalogenase

B: (S)-2-haloacid dehalogenase

hetero molecules

54.9 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)	66.300, 84.749, 92.851
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	(S)-2-haloacid dehalogenase Mass: 27411.088 Da / Num. of mol.: 2 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-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.38 Å³/Da / Density % sol: 48.3 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Potassium formate, 20% 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: Jun 23, 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: 2.02→38.55 Å / Num. obs: 34818 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.084 / R_pim(I) all: 0.037 / R_rim(I) all: 0.092 / Χ²: 0.94 / Net I/σ(I): 11.3 / Num. measured all: 216051
Reflection shell	Resolution: 2.02→2.07 Å / % possible obs: 99 % / Redundancy: 5.5 % / R_merge(I) obs: 0.954 / Num. measured all: 13830 / Num. unique obs: 2517 / CC_1/2: 0.817 / R_pim(I) all: 0.475 / R_rim(I) all: 1.071 / Χ²: 0.91 / Net I/σ(I) obs: 2.4

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.02→30.872 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.235	1655	4.89 %
R_work	0.2064	-	-
obs	0.2078	33877	96.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.02→30.872 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3718	0	1	244	3963

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3805
X-RAY DIFFRACTION	f_angle_d	0.548	5164
X-RAY DIFFRACTION	f_dihedral_angle_d	5.886	2263
X-RAY DIFFRACTION	f_chiral_restr	0.038	568
X-RAY DIFFRACTION	f_plane_restr	0.003	662

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 (%)
2.02-2.0795	0.3961	124	0.3374	2530	X-RAY DIFFRACTION	93
2.0795-2.1466	0.3088	161	0.2716	2683	X-RAY DIFFRACTION	99
2.1466-2.2233	0.3677	136	0.3064	2530	X-RAY DIFFRACTION	93
2.2233-2.3123	0.4137	109	0.3751	2227	X-RAY DIFFRACTION	82
2.3123-2.4175	0.2587	137	0.2261	2757	X-RAY DIFFRACTION	100
2.4175-2.5449	0.2697	132	0.2212	2730	X-RAY DIFFRACTION	99
2.5449-2.7042	0.2451	146	0.234	2740	X-RAY DIFFRACTION	100
2.7042-2.9129	0.275	120	0.2223	2788	X-RAY DIFFRACTION	100
2.9129-3.2057	0.2538	165	0.2181	2732	X-RAY DIFFRACTION	100
3.2057-3.6689	0.216	129	0.2093	2774	X-RAY DIFFRACTION	99
3.6689-4.62	0.1717	136	0.1666	2808	X-RAY DIFFRACTION	99
4.62-30.87	0.1984	160	0.159	2923	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	9.1503	3.4061	6.8854	3.7828	3.3627	8.96	0.0432	0.7635	-0.1775	-0.1931	0.0255	-0.1109	-0.1225	0.5782	-0.0868	0.2554	0.0204	0.0132	0.2816	-0.0083	0.2516	1.9677	5.2239	12.083
2	7.8469	-1.5255	2.7769	6.1139	-1.5558	1.5497	-0.0344	-1.0798	0.6272	0.5568	-0.0175	-0.3118	-0.0096	0.2255	0.1253	0.3237	-0.0228	-0.0224	0.5197	-0.03	0.3041	18.3383	0.7944	33.0308
3	8.0377	5.0433	5.6025	4.9009	6.1041	7.3576	-0.1614	0.9619	-0.2305	-1.1229	0.3655	0.0627	-1.0905	0.905	-0.1702	0.4295	0.0423	-0.0049	0.437	-0.0454	0.36	19.6066	-6.7344	18.7217
4	5.9377	2.0281	2.6949	6.3491	1.8317	7.4842	0.4102	0.9387	-0.8847	-0.203	0.0238	0.0752	0.742	0.3931	-0.4545	0.3216	0.0874	-0.0372	0.3773	-0.0406	0.4279	15.4522	-14.0402	20.0165
5	4.6854	-3.8274	2.3287	4.7321	-1.7364	2.5241	-0.0538	-0.3968	0.0079	0.3863	0.1216	-0.1752	0.0401	-0.0472	-0.0316	0.2862	-0.0408	-0.0178	0.3753	0.009	0.2758	9.8781	-0.5555	26.9247
6	2.1663	-0.2688	0.566	2.1673	-0.4821	2.1262	0.0402	0.1834	-0.1922	-0.2248	-0.1226	-0.036	0.0626	-0.0386	0.0479	0.2462	0.0106	-0.013	0.2763	-0.0212	0.3429	-0.7284	-1.338	10.9328
7	3.7129	0.9387	1.6757	3.8079	2.057	7.1999	-0.1019	0.4877	-0.122	-0.2773	0.089	-0.3627	-0.0095	0.5146	0.0572	0.2865	0.0272	0.0567	0.3106	0.036	0.2969	11.3898	9.0471	6.6066
8	1.4414	0.5345	1.111	8.7188	1.178	5.4881	-0.0944	-0.4256	0.7274	0.2303	-0.2835	0.5426	-1.1319	-0.9684	0.3814	0.3875	0.0971	0.0218	0.3874	-0.0081	0.292	-1.9236	17.9078	11.6079
9	7.1551	-2.0834	6.4747	5.1644	-2.5502	9.1762	0.3593	-0.1687	-0.6065	0.1446	0.0893	0.3572	0.1951	-0.4138	-0.4436	0.2862	-0.0115	0.0737	0.3043	0.0319	0.4806	-16.997	-9.3532	23.1558
10	1.9947	-1.4612	2.2473	6.5677	-3.3903	4.318	-0.9297	0.2032	0.4732	-1.1303	0.8053	0.9422	-1.1314	-2.4141	0.0769	0.7344	0.0364	-0.1952	0.9848	-0.0437	0.7611	-35.1375	-0.5678	5.6232
11	6.6745	1.5439	-2.0469	8.6333	1.8885	7.7911	-0.1356	0.5871	-0.093	-0.3479	-0.1578	0.9131	1.8232	-0.6237	0.1606	0.8521	-0.086	-0.099	0.7187	-0.1048	0.6386	-26.0432	-10.8447	0.1356
12	2.7316	0.5985	0.4625	1.6261	-0.8328	2.192	-0.0568	0.1064	-0.1465	-0.0722	-0.0142	0.0017	0.0885	-0.0401	0.0814	0.2018	0.009	0.0035	0.2406	-0.0514	0.3784	-13.443	-8.7213	19.9404
13	6.6819	-2.432	1.9449	1.7232	-1.3138	3.6482	0.0782	-0.5536	-0.6377	-0.0259	0.0497	0.3885	0.097	-0.3498	-0.1129	0.2804	-0.0322	0.0369	0.3161	-0.0023	0.497	-23.7607	-15.1422	27.54

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 41 through 55 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 56 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 96 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 97 through 119 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 120 through 155 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 156 through 221 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 264 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 265 through 276 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 41 through 55 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 56 through 78 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 79 through 139 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 221 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 222 through 276 )

-
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