PDB-6nkf: Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome.

ID or keywords:

Entry

Database: PDB / ID: 6nkf

Title

Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome.

Components

Lip_vut4, C3L

Keywords

HYDROLASE / Lipase / goat rumen metagenomics

Function / homology

: / BD-FAE / lipase activity / : / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / 2-BUTANOL / Esterase/lipase/thioesterase

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.232 Å

Authors

Kim, Y. / Welk, L. / Mukendi, G. / Nkhi, G. / Motloi, T. / Jedrzejczak, R. / Feto, N. / Joachimiak, A.

Citation

Journal: To Be Published
Title: Crystal Structure of the Lipase Lip_vut4 from Goat Rumen metagenome.
Authors: Kim, Y. / Welk, L. / Jedrzejczak, R. / Feto, A. / Joachimiak, A.

History

Deposition	Jan 7, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6nkf.cif.gz	498.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6nkf.ent.gz	415.4 KB	Display	PDB format
PDBx/mmJSON format	6nkf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6nkf_validation.pdf.gz	482.8 KB	Display	wwPDB validaton report
Full document	6nkf_full_validation.pdf.gz	487.2 KB	Display
Data in XML	6nkf_validation.xml.gz	49.5 KB	Display
Data in CIF	6nkf_validation.cif.gz	70.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/6nkf ftp://data.pdbj.org/pub/pdb/validation_reports/nk/6nkf	HTTPS FTP

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Related structure data

Similar structure data	2rj4-2 4frq-1 5m7b-1 3sx7-2 3v0o-d 3v0m-d 5m7d-1 5c1g-1 3sxg-2 5b7y-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Lip_vut4, C3L

B: Lip_vut4, C3L

C: Lip_vut4, C3L

D: Lip_vut4, C3L

hetero molecules

140 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lip_vut4, C3L

D: Lip_vut4, C3L

hetero molecules

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

2

B: Lip_vut4, C3L

C: Lip_vut4, C3L

hetero molecules

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

Unit cell

Length a, b, c (Å)	157.856, 157.856, 195.492
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Lip_vut4, C3L Mass: 34466.910 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q65FG3*PLUS
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-SBT / 2-BUTANOL Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H₂O
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: 4.42 Å³/Da / Density % sol: 72.15 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2 M sodium thiocyanate pH 6.9, 20 % (w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.23→50 Å / Num. obs: 119411 / % possible obs: 100 % / Redundancy: 9.9 % / B_iso Wilson estimate: 43.9 Å² / CC_1/2: 0.986 / R_merge(I) obs: 0.145 / Net I/σ(I): 25.4
Reflection shell	Resolution: 2.23→2.27 Å / Redundancy: 10.1 % / R_merge(I) obs: 0.99 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 5862 / CC_1/2: 0.844 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.232→42.723 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.38

	R_factor	Num. reflection	% reflection
R_free	0.1791	5991	5.02 %
R_work	0.1535	-	-
obs	0.1548	119305	99.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 49.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.232→42.723 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9461	0	114	674	10249

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	9908
X-RAY DIFFRACTION	f_angle_d	0.701	13430
X-RAY DIFFRACTION	f_dihedral_angle_d	15.221	5820
X-RAY DIFFRACTION	f_chiral_restr	0.048	1423
X-RAY DIFFRACTION	f_plane_restr	0.005	1763

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 (%)
2.2317-2.257	0.236	195	0.2002	3297	X-RAY DIFFRACTION	89
2.257-2.2836	0.2611	178	0.1965	3756	X-RAY DIFFRACTION	100
2.2836-2.3114	0.2252	188	0.1866	3728	X-RAY DIFFRACTION	100
2.3114-2.3407	0.2231	200	0.1822	3756	X-RAY DIFFRACTION	100
2.3407-2.3715	0.194	191	0.1751	3780	X-RAY DIFFRACTION	100
2.3715-2.404	0.2133	193	0.1742	3709	X-RAY DIFFRACTION	100
2.404-2.4383	0.2148	187	0.1712	3795	X-RAY DIFFRACTION	100
2.4383-2.4747	0.2048	195	0.1725	3758	X-RAY DIFFRACTION	100
2.4747-2.5134	0.204	188	0.1694	3743	X-RAY DIFFRACTION	100
2.5134-2.5546	0.2128	204	0.1702	3748	X-RAY DIFFRACTION	100
2.5546-2.5986	0.2231	180	0.1668	3783	X-RAY DIFFRACTION	100
2.5986-2.6458	0.2045	174	0.1667	3786	X-RAY DIFFRACTION	100
2.6458-2.6967	0.2014	216	0.1674	3733	X-RAY DIFFRACTION	100
2.6967-2.7518	0.2137	220	0.1711	3759	X-RAY DIFFRACTION	100
2.7518-2.8116	0.2046	224	0.1758	3714	X-RAY DIFFRACTION	100
2.8116-2.877	0.2257	212	0.1711	3770	X-RAY DIFFRACTION	100
2.877-2.9489	0.1884	220	0.1671	3757	X-RAY DIFFRACTION	100
2.9489-3.0286	0.2023	179	0.1682	3807	X-RAY DIFFRACTION	100
3.0286-3.1177	0.2087	212	0.1793	3751	X-RAY DIFFRACTION	100
3.1177-3.2183	0.2129	197	0.1732	3801	X-RAY DIFFRACTION	100
3.2183-3.3333	0.1938	196	0.1728	3785	X-RAY DIFFRACTION	100
3.3333-3.4667	0.196	169	0.1734	3811	X-RAY DIFFRACTION	100
3.4667-3.6244	0.2058	215	0.1657	3782	X-RAY DIFFRACTION	100
3.6244-3.8154	0.1699	208	0.1518	3823	X-RAY DIFFRACTION	100
3.8154-4.0542	0.1768	206	0.1325	3823	X-RAY DIFFRACTION	100
4.0542-4.367	0.1352	181	0.1216	3843	X-RAY DIFFRACTION	100
4.367-4.8059	0.1235	197	0.113	3853	X-RAY DIFFRACTION	100
4.8059-5.5001	0.1388	216	0.1268	3866	X-RAY DIFFRACTION	100
5.5001-6.9248	0.1482	204	0.1487	3937	X-RAY DIFFRACTION	100
6.9248-42.7309	0.1718	246	0.151	4060	X-RAY DIFFRACTION	100

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	1.6191	-1.3169	1.0558	2.7746	-1.0654	1.9531	-0.0358	0.1674	0.1841	-0.0002	0.0152	-0.107	-0.3017	0.2007	0.0203	0.3289	-0.0675	0.0258	0.3169	0.0066	0.2585	34.0832	98.6994	-3.8008
2	1.5392	0.1623	-0.0842	2.7472	-1.2687	2.8449	0.0189	0.0708	0.0767	-0.1907	0.0872	0.209	-0.0011	-0.0698	-0.1099	0.3185	-0.0112	-0.0356	0.2938	0.0208	0.3131	21.4202	92.7623	-6.4589
3	4.6474	1.3581	-0.9535	2.8746	0.9512	5.2127	-0.0401	-0.0518	-0.3163	-0.0288	0.2157	-0.1724	0.4701	0.3923	-0.0971	0.4115	0.0189	-0.0263	0.3225	-0.009	0.3641	34.6242	76.8896	3.4371
4	4.2906	-4.2185	-1.9416	5.9349	3.0515	2.2752	-0.0222	0.1204	-0.178	0.1304	-0.2245	0.57	0.0594	-0.2643	0.1906	0.3305	-0.0494	-0.0059	0.3081	0.0726	0.345	14.8181	68.6152	-3.0555
5	3.8361	-0.2106	-1.5357	1.8489	0.1733	1.896	0.1102	0.2256	-0.1666	-0.2536	-0.097	0.2564	0.0942	-0.3053	0.0631	0.361	-0.0306	-0.0872	0.3322	-0.0129	0.3125	25.4694	53.509	-16.0982
6	2.6007	-0.8988	-1.2179	0.9685	0.3576	1.658	0.0152	0.4673	-0.2104	-0.315	-0.0982	0.1939	0.031	-0.3964	-0.0011	0.4198	0.012	-0.0567	0.3914	-0.0212	0.3444	33.4351	50.522	-27.7369
7	1.8634	-0.7209	-0.6495	2.3605	0.5108	1.5851	0.1243	0.1472	0.1384	-0.2484	-0.1034	-0.1944	-0.1747	0.0714	0.0903	0.397	0.0031	0.032	0.3333	0.021	0.3423	50.2365	50.7794	-28.1266
8	1.8157	-0.7284	-1.2069	3.0565	0.1855	6.3363	0.2104	0.0994	0.3857	-0.4973	-0.0011	-0.108	-0.6766	0.0917	-0.0042	0.4511	-0.0213	0.0485	0.3287	0.0007	0.457	46.9847	63.643	-22.3872
9	3.7386	1.7491	1.5538	2.6138	-0.5168	3.5745	0.1301	0.1959	0.4725	-0.2877	-0.1172	0.1434	-0.764	-0.2826	-0.0502	0.5144	0.1046	0.036	0.3206	0.0303	0.468	34.516	68.9289	-22.3082
10	7.8571	4.8446	-5.1079	5.6702	-3.3321	7.2705	0.3219	-0.6	0.5167	-0.2055	-0.3534	-0.2811	-0.4822	0.6903	-0.0114	0.3923	0.0295	0.0487	0.2943	-0.0288	0.4638	44.4716	63.5518	-12.7953
11	3.4608	-0.7843	-0.9759	1.8608	0.502	1.5817	0.0154	0.0061	-0.0855	0.025	-0.0054	0.142	0.0858	-0.0667	-0.018	0.3299	-0.0313	-0.0423	0.29	0.0311	0.2762	29.147	52.7014	0.1689
12	2.902	-0.4289	-0.3814	2.104	-0.2349	1.5302	-0.0943	-0.1296	-0.3797	0.1328	0.1192	0.4702	0.251	-0.2043	-0.0075	0.2888	-0.0347	0.0291	0.3112	0.0571	0.3777	16.2026	52.2318	10.9922
13	2.0211	-0.1073	-0	2.6195	-0.7523	2.3283	-0.0496	-0.1299	-0.0591	0.2332	0.0922	0.2234	-0.0866	-0.1356	-0.1192	0.2543	-0.0062	0.0206	0.2612	0.0086	0.3235	15.9332	65.766	11.7339
14	5.7903	3.6452	4.1475	3.111	2.5255	5.7659	0.09	-0.3969	0.0556	0.129	-0.1027	0.2084	-0.1002	-0.523	0.0362	0.3622	0.0682	0.0483	0.3768	0.0243	0.3895	20.2751	87.8153	9.2571
15	4.3999	-0.5698	1.844	1.8936	-0.7476	2.4276	-0.0476	-0.2301	0.3828	0.257	0.08	0.0119	-0.2758	-0.0293	-0.0401	0.4307	-0.0203	0.0169	0.3606	-0.0719	0.267	35.6555	94.2927	24.7382
16	3.8923	-0.0491	2.0127	1.0014	-0.293	2.125	-0.0526	-0.3461	0.1819	0.3599	0.0627	-0.1289	-0.3257	-0.0582	-0.0074	0.6069	-0.0308	-0.0242	0.5279	-0.1152	0.3524	45.9886	91.6698	37.7438
17	4.1821	2.0881	3.4014	3.3268	2.39	4.1321	-0.0265	-0.558	0.2081	0.1233	-0.0299	0.0205	-0.1639	-0.3686	0.0638	0.5897	-0.0241	-0.0641	0.5369	-0.0364	0.3324	48.2491	84.1206	45.0928
18	3.5703	0.9306	-0.6814	3.8591	0.7057	5.8684	0.0896	-0.3418	-0.283	0.5533	0.01	-0.2124	0.4054	0.0634	-0.1102	0.5328	-0.0201	-0.1371	0.4687	0.0021	0.3725	49.1377	74.3906	36.8986
19	3.5103	-4.0383	-4.9209	7.1893	4.3442	7.5597	0.0612	0.1111	-0.4999	0.1451	-0.0681	0.4369	0.0552	-0.4252	-0.0262	0.4691	-0.117	-0.0432	0.5629	0.0151	0.4117	33.1284	76.7277	31.2965
20	1.6088	-0.8523	1.2933	2.1408	-1.2092	3.2339	0.0569	0.0998	0.069	0.1444	-0.0521	-0.1697	0.0198	0.2611	0.0163	0.3435	-0.0585	0.0029	0.3816	-0.0433	0.3319	42.9518	86.9347	13.0329

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 90 through 213 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 214 through 278 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 279 through 303 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 2 through 23 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 24 through 89 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 90 through 188 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 189 through 258 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 259 through 278 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 279 through 296 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 2 through 23 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 24 through 89 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 90 through 213 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 214 through 302 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 2 through 23 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 24 through 89 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 90 through 213 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 214 through 238 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 239 through 278 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 279 through 296 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 2 through 89 )

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