PDB-8vb3: Dienelactone hydrolase from Solimonas fluminis

ID or keywords:

Entry

Database: PDB / ID: 8vb3

Title

Dienelactone hydrolase from Solimonas fluminis

Components

Dienelactone hydrolase

Keywords

HYDROLASE / dienelactone / metagenomic / Solimonas fluminis / esterase

Function / homology

Dienelactone hydrolase / Dienelactone hydrolase family / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Dienelactone hydrolase

Function and homology information

Biological species

Solimonas fluminis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Schnettler Fernandez, J.D.F. / Campbell, E.C. / Hollfelder, F.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Metal-independent organophosphate hydrolysis in a protein family possessing a catalytic triad
Authors: Schnettler Fernandez, J.D.F. / Campbell, E.C. / Khashiev, R. / Klein, J.O. / Hollfelder, F.

History

Deposition	Dec 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vb3.cif.gz	247.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8vb3.ent.gz	164 KB	Display	PDB format
PDBx/mmJSON format	8vb3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vb/8vb3 ftp://data.pdbj.org/pub/pdb/validation_reports/vb/8vb3	HTTPS FTP

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Related structure data

Similar structure data	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

Deposited unit

A: Dienelactone hydrolase

B: Dienelactone hydrolase

hetero molecules

55.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dienelactone hydrolase

hetero molecules

B: Dienelactone hydrolase

hetero molecules

defined by author&software
55.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.143, 87.835, 71.415
Angle α, β, γ (deg.)	90.000, 99.170, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Dienelactone hydrolase Mass: 27187.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solimonas fluminis (bacteria) / Gene: C3942_20560 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S5TB63
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.19 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% w/v PEG3000, 0.1 M Tris, pH 7, 0.2 M calcium acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.45→39.63 Å / Num. obs: 86395 / % possible obs: 99.73 % / Redundancy: 6.5 % / B_iso Wilson estimate: 15.15 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.0669 / R_pim(I) all: 0.02808 / Net I/σ(I): 12.01
Reflection shell	Resolution: 1.45→1.502 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.2875 / Mean I/σ(I) obs: 4.43 / Num. unique obs: 8555 / CC_1/2: 0.979 / R_pim(I) all: 0.1235 / % possible all: 99.14

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→39.63 Å / SU ML: 0.115 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.4499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1861	4382	5.08 %
R_work	0.1579	81830	-
obs	0.1593	86212	99.74 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.11 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→39.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3658	0	61	314	4033

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0154	3893
X-RAY DIFFRACTION	f_angle_d	1.5195	5308
X-RAY DIFFRACTION	f_chiral_restr	0.112	566
X-RAY DIFFRACTION	f_plane_restr	0.0143	715
X-RAY DIFFRACTION	f_dihedral_angle_d	13.1834	558

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 (%)
1.45-1.47	0.2309	145	0.1829	2697	X-RAY DIFFRACTION	99.02
1.47-1.48	0.1947	149	0.1807	2712	X-RAY DIFFRACTION	99.2
1.48-1.5	0.2005	152	0.1759	2653	X-RAY DIFFRACTION	99.22
1.5-1.52	0.1909	145	0.1714	2716	X-RAY DIFFRACTION	99.2
1.52-1.54	0.2143	165	0.1665	2710	X-RAY DIFFRACTION	99.21
1.54-1.56	0.2215	149	0.1711	2667	X-RAY DIFFRACTION	99.65
1.56-1.58	0.2005	158	0.1628	2733	X-RAY DIFFRACTION	99.38
1.58-1.61	0.1832	156	0.1526	2728	X-RAY DIFFRACTION	99.79
1.61-1.63	0.1933	114	0.15	2723	X-RAY DIFFRACTION	99.68
1.63-1.66	0.1643	108	0.1415	2776	X-RAY DIFFRACTION	99.72
1.66-1.69	0.1735	134	0.1458	2719	X-RAY DIFFRACTION	99.69
1.69-1.72	0.2382	130	0.1575	2717	X-RAY DIFFRACTION	99.86
1.72-1.75	0.1873	150	0.1483	2771	X-RAY DIFFRACTION	99.8
1.75-1.79	0.1727	141	0.1512	2682	X-RAY DIFFRACTION	99.93
1.79-1.83	0.1631	160	0.1536	2763	X-RAY DIFFRACTION	99.93
1.83-1.87	0.1879	149	0.1623	2683	X-RAY DIFFRACTION	99.93
1.87-1.92	0.2076	136	0.1643	2756	X-RAY DIFFRACTION	99.69
1.92-1.97	0.189	146	0.1545	2699	X-RAY DIFFRACTION	99.86
1.97-2.03	0.1549	147	0.147	2721	X-RAY DIFFRACTION	99.83
2.03-2.09	0.1829	153	0.1454	2750	X-RAY DIFFRACTION	100
2.09-2.17	0.187	150	0.1563	2726	X-RAY DIFFRACTION	99.93
2.17-2.25	0.1778	142	0.1562	2741	X-RAY DIFFRACTION	99.97
2.25-2.36	0.1867	155	0.1509	2738	X-RAY DIFFRACTION	99.93
2.36-2.48	0.1821	142	0.1662	2730	X-RAY DIFFRACTION	100
2.48-2.63	0.1932	151	0.1698	2749	X-RAY DIFFRACTION	100
2.63-2.84	0.1861	146	0.1719	2740	X-RAY DIFFRACTION	99.97
2.84-3.12	0.1947	144	0.1684	2735	X-RAY DIFFRACTION	99.93
3.12-3.57	0.1844	153	0.1595	2737	X-RAY DIFFRACTION	100
3.58-4.5	0.1759	146	0.1403	2774	X-RAY DIFFRACTION	99.97
4.5-39.63	0.1899	166	0.1621	2784	X-RAY DIFFRACTION	99.86

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	0.392638871474	0.0473032262231	-0.0816650290878	0.0773607672912	0.100030923843	0.184930906234	0.0663189210149	0.188662565715	-0.238160698194	-0.100733210763	-0.108146886298	0.159689575627	0.17359852463	0.0766308779446	-0.0126138206193	0.228894941263	0.00341839855755	-0.0178841065532	0.224378594693	-0.0282813812721	0.19659053113	-7.80721873829	-12.7694571738	8.87410116637
2	0.479578761664	-0.149887145282	0.0572869524271	0.345835203119	0.244654535857	0.376282727474	0.1032566883	0.207769301581	-0.0536145835147	-0.055042112906	-0.00144878577455	-0.0645763796211	0.0812580680357	0.171207122591	0.0645208746038	0.162630273415	0.00858088308951	-0.0033100989118	0.242646385643	-0.00515403780953	0.125944304085	-1.11811585618	-4.96107547204	12.3977349847
3	0.0644690370276	-0.0463896289278	0.00886182750398	0.189831618117	0.101980085561	0.080614919972	0.020363324899	0.152806676677	0.234458858552	-0.242317941446	0.1350218815	0.0483676513836	-0.0635898672132	-0.0548929896917	0.0975993355822	0.302410047606	0.0282786080786	0.113452024837	0.561008505468	0.202494831429	0.346309687503	-2.97527465775	12.5567879473	7.0056258247
4	0.923639757967	-0.218649922686	-0.0904188754697	0.214336920367	0.1579188947	0.689961517541	0.0779941294587	0.19010802722	0.129315733815	-0.0187484675589	-0.0259857258852	-0.0117542369562	-0.0509696163577	-0.0163813557816	0.0609941940882	0.118804831234	0.0115739292475	0.0113012570357	0.150523007304	0.0278859820768	0.132803485674	-8.52485178284	4.89855438749	21.987494236
5	0.337512231567	0.00115639946375	0.202089768946	0.303525231472	0.384255053515	0.462802315991	0.062861401456	0.33487663591	-0.000968136002059	0.0359849346968	0.0776615906713	-0.0199191318178	0.128847958488	0.0663046448082	0.0808585925472	0.139806426817	0.0132042598903	-0.00931329414424	0.21024445119	-0.000100541373623	0.141329734215	3.28977739023	-2.13350907384	24.5739194397
6	0.306772254695	-0.0828799443156	-0.0410823170249	0.0711225441078	-0.0782098627096	0.128730770512	-0.0937589795639	-0.615366607959	-0.127687590359	0.245896411536	0.294156657671	-0.0530257706361	0.12303205092	-0.289261017987	0.00298944412708	0.256620369573	0.0294392727782	-0.0430671383655	0.380578220781	0.0375916522956	0.192771510211	6.76514110956	-5.71281680458	65.9077016061
7	0.0565105316266	0.00641310824968	-0.0322143472594	0.0379287789768	-0.00482648874434	0.0879481990763	0.110727720826	-0.197437235446	-0.535804439431	0.241954866465	-0.118317850067	0.0830135246892	0.137849232168	-0.162120950726	-0.00192622636903	0.203609467404	-0.0139121182159	-0.0539262836388	0.167882316804	0.0274096411604	0.375132381317	8.40660142947	-13.7491686778	52.4593065002
8	0.221166820502	0.00401102927055	0.14061885648	0.132639625404	0.0365257347872	0.267780344698	0.047671799267	-0.212480361138	-0.18139135727	-0.144087020584	0.156662247205	0.178981468163	0.068659260661	-0.478895725247	0.0442870345866	0.176732545374	-0.040376583956	-0.0224352006222	0.303213821947	0.0630518233137	0.201228473408	-2.75884852687	-5.3293907379	55.600695297
9	0.63051915763	-0.0677961547418	0.142160022334	0.581306880737	-0.156074716525	0.697966973904	-0.0752565110935	-0.390868114587	0.0678015377724	0.0619357646656	0.301513185799	0.0489421710685	-0.0847461322135	-0.210364484241	0.24376548876	0.203812740135	0.0563542001384	0.00455507055642	0.362700301849	-0.0209355166723	0.190743645648	0.558073344994	5.34401094471	61.7646117719
10	0.0480093408675	0.0153582861399	0.0073294568676	0.0307691297284	-0.0157610765535	-0.00485218549088	0.053324227139	-0.257576282796	0.0739750700851	0.0769458873977	4.45697672153E-5	-0.176318775426	-0.0210181244654	0.164681024852	-0.000415647610669	0.178018521854	4.28411106494E-5	-0.0219109377073	0.28335517247	-0.0503312605992	0.170258497129	13.8391917046	4.09198946954	57.9050598411
11	0.620588050132	0.0722549020195	0.345870234502	0.267286791925	-0.0194505410656	0.699324674334	0.0341695763462	-0.0676186564937	0.084100119658	0.0149066019845	-0.00300719370763	-0.0212460423015	-0.0322755081704	-0.0165104706561	0.160889184582	0.127258811485	-0.00453906295171	0.00783266973975	0.14388176791	-0.0256743925833	0.15511017839	5.67415343509	6.39111688375	45.6865418595
12	0.0276636325477	-0.0244324593895	0.00572662206193	0.0392837066671	-0.0645308815521	0.0935026776041	0.0751927621705	-0.456237388	0.150703206083	0.0586263589611	-0.0519974917828	0.0141474294644	-0.0378279634155	-0.0594631354231	0.00122547296338	0.159007794362	-0.0151333094335	0.0178285124355	0.325266954258	-0.0444223806339	0.176590460946	-13.8851988632	5.5983221251	51.933875354
13	0.0618094717538	-0.0709857327193	0.00111652612591	0.1937380266	-0.193024075444	0.221170157645	0.142169597663	0.0107802393526	-0.275211406979	-0.0984370892422	-0.00731156739454	0.144706187229	0.17933692697	-0.0281745453438	0.0716870959163	0.185397801444	0.00710930840214	-0.0411468640634	0.147886945128	-0.0296613456993	0.177333251419	1.01552571729	-5.67691575248	41.3487157383

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid -2 through 30 )	A	A	-2 - 30	1 - 33
2	2	chain 'A' and (resid 31 through 73 )	A	A	31 - 73	34 - 76
3	3	chain 'A' and (resid 74 through 87 )	A	A	74 - 87	77 - 90
4	4	chain 'A' and (resid 88 through 204 )	A	A	88 - 204	91 - 207
5	5	chain 'A' and (resid 205 through 238 )	A	A	205 - 238	208 - 241
6	6	chain 'B' and (resid 1 through 21 )	B	B	1 - 21	1 - 21
7	7	chain 'B' and (resid 22 through 35 )	B	B	22 - 35	22 - 35
8	8	chain 'B' and (resid 36 through 54 )	B	B	36 - 54	36 - 54
9	9	chain 'B' and (resid 55 through 87 )	B	B	55 - 87	55 - 87
10	10	chain 'B' and (resid 88 through 103 )	B	B	88 - 103	88 - 103
11	11	chain 'B' and (resid 104 through 204 )	B	B	104 - 204	104 - 204
12	12	chain 'B' and (resid 205 through 218 )	B	B	205 - 218	205 - 218
13	13	chain 'B' and (resid 219 through 238 )	B	B	219 - 238	219 - 238

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