PDB-3ojg: Structure of an inactive lactonase from Geobacillus kaustophilus ...

ID or keywords:

Entry

Database: PDB / ID: 3ojg

Title

Structure of an inactive lactonase from Geobacillus kaustophilus with bound N-butyryl-DL-homoserine lactone

Components

Phosphotriesterase

Keywords

HYDROLASE / (beta/alpha)8 barrel / lactonase

Function / homology

Function and homology information

Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function

Biological species

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Xue, B. / Chow, J.Y. / Tung, A. / Robinson, R.C.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Directed evolution of a thermostable quorum-quenching lactonase from the amidohydrolase superfamily
Authors: Chow, J.Y. / Xue, B. / Lee, K.H. / Tung, A. / Wu, L. / Robinson, R.C. / Yew, W.S.

History

Deposition	Aug 22, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 27, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Mar 26, 2014	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ojg.cif.gz	144.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3ojg.ent.gz	119.4 KB	Display	PDB format
PDBx/mmJSON format	3ojg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ojg_validation.pdf.gz	439.5 KB	Display	wwPDB validaton report
Full document	3ojg_full_validation.pdf.gz	439.8 KB	Display
Data in XML	3ojg_validation.xml.gz	16.4 KB	Display
Data in CIF	3ojg_validation.cif.gz	24.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/3ojg ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3ojg	HTTPS FTP

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Related structure data

Similar structure data	4h9y-d 4ha0-d 4xd3-d 4h9z-d 3wml-1 6g0m-1 4xay-d 4j35-2 6jsu-d 6g23-1 3c86-2 6g3m-1 4keu-2 6fvp-1 3htw-2 6jst-1 6gbk-d 4wvx-d 6jst-2 4kev-2 Search similar-shape structures by Omokage search (details) 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1)

Deposited unit

A: Phosphotriesterase

hetero molecules

37.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphotriesterase

hetero molecules

A: Phosphotriesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.269, 76.244, 134.408
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-355- HOH
2	1	A-392- HOH

#1: Protein	Phosphotriesterase Mass: 36878.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical	ChemComp-HL4 / N-[(3S)-2-oxotetrahydrofuran-3-yl]butanamide / N-butyryl-L-homoserine lactone Mass: 171.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₃NO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.44 Å³/Da / Density % sol: 49.61 % / Mosaicity: 0.5 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Tris, 20%(w/v) PEG 4000, 1.0mM ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13B1 / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2008 / Details: Inter-Frame Total Dead Time: 5s

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. all: 47658 / Num. obs: 45826 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / R_merge(I) obs: 0.092 / Χ²: 1.282 / Net I/σ(I): 11.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.6-1.63	5.4	0.43	2112	0.667	1	89.4
1.63-1.66	5.8	0.36	2097	0.679	1	89.1
1.66-1.69	5.8	0.306	2120	0.726	1	90.7
1.69-1.72	5.7	0.276	2141	0.755	1	90.3
1.72-1.76	5.7	0.225	2199	0.746	1	93.7
1.76-1.8	5.6	0.205	2213	0.813	1	93.7
1.8-1.85	5.5	0.166	2240	0.823	1	94.2
1.85-1.9	5.6	0.177	2274	1.061	1	97.3
1.9-1.95	5.5	0.138	2304	1.228	1	97.3
1.95-2.02	5.6	0.117	2297	1.205	1	97.7
2.02-2.09	5.6	0.111	2346	1.34	1	98.7
2.09-2.17	5.7	0.097	2338	1.357	1	98.6
2.17-2.27	5.7	0.091	2349	1.444	1	98.9
2.27-2.39	5.8	0.086	2364	1.397	1	99
2.39-2.54	5.9	0.086	2374	1.516	1	99.5
2.54-2.74	5.7	0.084	2385	1.634	1	99.5
2.74-3.01	6	0.078	2385	1.676	1	99.7
3.01-3.45	5.7	0.078	2414	2.047	1	99.6
3.45-4.34	5	0.077	2396	2.052	1	98
4.34-50	5.3	0.102	2478	2.168	1	97.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 28.75 / Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.5 Å	24.11 Å
Translation	3.5 Å	24.11 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.1.4	phasing
PHENIX	1.5_2	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→24.115 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8256 / SU ML: 0.22 / σ(F): 0.62 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2194	2302	5.04 %	RANDOM
R_work	0.1969	-	-	-
all	0.198	47658	-	-
obs	0.198	45678	95.26 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.959 Å² / k_sol: 0.383 e/Å³

Displacement parameters

B_iso max: 93.83 Å² / B_iso mean: 26.8211 Å² / B_iso min: 10.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.893 Å²	-0 Å²	0 Å²
2-	-	-3.876 Å²	-0 Å²
3-	-	-	8.769 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→24.115 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2543	0	14	263	2820

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2614
X-RAY DIFFRACTION	f_angle_deg	1.018	3536
X-RAY DIFFRACTION	f_chiral_restr	0.065	380
X-RAY DIFFRACTION	f_plane_restr	0.005	467
X-RAY DIFFRACTION	f_dihedral_angle_d	17.045	961

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5997-1.6568	0.2888	212	0.262	3685	3897	83
1.6568-1.7231	0.2844	200	0.2397	4091	4291	90
1.7231-1.8015	0.2505	218	0.2246	4199	4417	93
1.8015-1.8965	0.2742	209	0.2314	4320	4529	96
1.8965-2.0153	0.2545	247	0.211	4373	4620	97
2.0153-2.1708	0.2254	256	0.2075	4454	4710	98
2.1708-2.389	0.2323	231	0.2012	4483	4714	99
2.389-2.7343	0.2161	240	0.1992	4538	4778	99
2.7343-3.4434	0.2044	241	0.1936	4570	4811	99
3.4434-24.1177	0.1815	248	0.1644	4663	4911	98

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	0.8908	-0.2558	0.7222	0.267	-0.4214	0.8923	-0.1598	0.0309	0.7005	0.1451	-0.0478	-0.1769	-0.6575	0.0794	0.1499	0.1512	-0.0709	-0.0286	0.1623	-0.0203	0.3659	27.4912	7.162	-23.7881
2	1.1392	-0.0248	0.3197	0.1231	0.0585	0.1243	0.047	0.0559	0.3286	-0.0583	-0.0737	-0.0003	-0.0448	-0.0126	0.0882	0.1469	0.0008	-0.0087	0.1364	-0.0421	0.1326	3.4724	-0.6765	-23.3426
3	1.9982	-1.2498	0.4481	2.0487	1.5708	2.8049	-0.3146	-0.4479	1.132	0.0581	-0.1526	0.4214	-0.9266	-0.3722	0.4203	0.3255	0.0331	0.0004	0.1778	-0.1665	0.6525	0.2644	10.6441	-20.6356
4	2.9213	-1.1486	-2.1585	1.9701	0.972	2.2664	-0.1865	-0.8141	0.5656	0.6272	-0.042	0.1839	0.1646	0.1784	-0.2329	0.1587	-0.0116	-0.0078	0.2381	-0.2176	0.1767	12.1135	8.5245	-11.2153
5	0.4172	0.1181	-0.0347	0.0428	-0.0425	0.1161	0.006	-0.127	0.3388	0.0436	-0.0343	-0.0027	0.0177	-0.1162	0.0569	0.1771	-0.0209	-0.0147	0.1205	-0.0429	0.2028	13.1829	2.495	-24.3208
6	2.5454	-0.5567	-1.3777	1.0682	-1.4199	4.2342	-0.0973	-0.0323	1.1344	-0.1145	0.3296	0.3668	-0.8861	-0.4558	-0.2964	0.266	0.036	-0.0477	0.1167	-0.0802	0.5215	13.2598	14.2005	-21.98
7	0.766	-0.078	-0.0045	0.0211	-0.0576	0.2549	-0.0389	0.0316	0.0719	-0.066	-0.0065	-0.0321	0.0399	-0.0785	0.0295	0.1613	-0.0152	0.0002	0.1061	0.0043	0.1542	10.6335	-4.2235	-29.9726
8	3.6794	-1.7975	0.9928	2.0225	0.6972	1.4892	0.1149	0.2602	-0.7924	0.6992	0.0281	0.1436	0.2349	0.2781	-0.1879	0.1653	-0.0138	-0.047	0.0894	-0.004	0.165	5.7476	-11.8223	-45.8406
9	1.7593	-0.143	-0.5216	0.8954	-0.2712	0.4831	0.0971	0.458	0.0617	-0.1682	-0.0192	-0.2958	0.1099	0.046	-0.0042	0.19	-0.0049	0.0173	0.1974	0.0172	0.1183	16.3775	-4.1783	-42.6088
10	0.4722	-0.0732	0.2765	0.9444	0.3203	0.5188	-0.0407	0.027	0.243	0.0394	0.0435	0.2189	-0.0466	0.0624	0.0165	0.1294	-0.0162	-0.0024	0.1324	0.0208	0.2298	16.2501	0.3788	-32.8776
11	1.4739	-0.5815	-0.2877	0.3661	-0.6499	4.627	0.1386	0.2752	-0.6494	-0.4659	-0.1013	0.0898	0.6356	-0.1325	0.0121	0.2017	0.0164	-0.035	0.0855	-0.016	0.252	11.1418	-21.6405	-32.3555
12	1.4527	0.0284	0.3441	1.0153	0.1059	0.091	0.0097	0.4709	-0.094	-0.2228	0.0446	-0.029	0.158	0.0216	-0.0388	0.1456	0.0167	0.0269	0.1569	0.0039	0.1012	20.5348	-9.9278	-37.0431
13	1.3544	0.0002	0.5032	0.7535	-0.3468	0.7864	0.1274	-0.0321	-0.2153	0.0539	-0.0395	-0.1173	-0.1042	0.0457	-0.0957	0.161	0.0013	-0.0027	0.1524	0.0089	0.1508	21.0994	-17.4311	-24.6191
14	1.7272	-0.2132	-0.3321	0.5102	-0.4048	0.6731	0.187	-0.344	-0.4191	0.097	-0.1337	0.118	-0.1373	-0.2404	-0.039	0.1479	0.0179	-0.0135	0.2276	-0.0082	0.0967	17.8421	-14.9261	-17.2058
15	1.3169	0.3918	-0.4803	0.9548	-0.6113	0.4379	-0.1299	-1.2116	-0.5282	0.5393	0.2917	0.2551	0.0569	-0.2353	-0.099	0.3464	-0.014	-0.0049	0.3432	0.0832	0.1475	15.7729	-17.6507	-6.9034
16	0.2347	0.0663	0.4965	0.5411	0.0379	1.0699	-0.0047	0.0507	0.02	0.1071	0.1927	-0.1912	-0.0946	-0.0706	-0.1048	0.1992	0.0142	-0.0562	0.278	0.0044	0.1651	28.833	-15.263	-11.7456
17	2.4161	-0.3818	-0.2459	0.7438	0.2704	0.3801	-0.1135	-0.636	0.0401	0.242	0.1041	0.0629	0.1249	0.1135	-0.0467	0.1589	0.0048	0.0274	0.1916	-0.0411	0.0778	2.1721	-4.7199	-14.8103
18	1.8448	-0.663	0.2627	0.453	-0.0646	0.1293	-0.2401	-0.892	0.0336	0.2561	0.2129	0.1195	0.0162	-0.1235	-0.0248	0.2209	-0.0107	0.0207	0.4102	-0.0486	0.0663	12.2211	-6.2231	-5.515
19	3.1368	0.3924	0.7697	2.2368	1.1863	0.732	-0.1905	-0.9941	0.3028	0.7022	-0.256	-0.3153	-0.2631	0.4983	0.3365	0.3501	0.0324	-0.1078	0.595	-0.0444	0.2609	29.1191	-9.0078	-0.8533
20	1.2812	-0.1647	0.3528	1.1089	0.7984	1.1038	-0.1009	-0.3284	0.4261	0.287	0.1623	-0.1481	0.0335	-0.2488	-0.0196	0.1973	-0.025	-0.0246	0.1949	-0.0606	0.2399	29.5466	-3.7891	-15.68

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 3:19)	A	3 - 19
2	X-RAY DIFFRACTION	2	(chain A and resid 20:41)	A	20 - 41
3	X-RAY DIFFRACTION	3	(chain A and resid 42:47)	A	42 - 47
4	X-RAY DIFFRACTION	4	(chain A and resid 48:61)	A	48 - 61
5	X-RAY DIFFRACTION	5	(chain A and resid 62:81)	A	62 - 81
6	X-RAY DIFFRACTION	6	(chain A and resid 82:87)	A	82 - 87
7	X-RAY DIFFRACTION	7	(chain A and resid 88:109)	A	88 - 109
8	X-RAY DIFFRACTION	8	(chain A and resid 110:114)	A	110 - 114
9	X-RAY DIFFRACTION	9	(chain A and resid 115:131)	A	115 - 131
10	X-RAY DIFFRACTION	10	(chain A and resid 132:149)	A	132 - 149
11	X-RAY DIFFRACTION	11	(chain A and resid 150:155)	A	150 - 155
12	X-RAY DIFFRACTION	12	(chain A and resid 156:175)	A	156 - 175
13	X-RAY DIFFRACTION	13	(chain A and resid 176:217)	A	176 - 217
14	X-RAY DIFFRACTION	14	(chain A and resid 218:240)	A	218 - 240
15	X-RAY DIFFRACTION	15	(chain A and resid 241:248)	A	241 - 248
16	X-RAY DIFFRACTION	16	(chain A and resid 249:262)	A	249 - 262
17	X-RAY DIFFRACTION	17	(chain A and resid 263:282)	A	263 - 282
18	X-RAY DIFFRACTION	18	(chain A and resid 283:302)	A	283 - 302
19	X-RAY DIFFRACTION	19	(chain A and resid 303:310)	A	303 - 310
20	X-RAY DIFFRACTION	20	(chain A and resid 311:325)	A	311 - 325

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Yorodumi