PDB-6nkd: Crystal Structure of the Lipase Lip_vut3 from Goat Rumen metagenome.

ID or keywords:

Entry

Database: PDB / ID: 6nkd

Title

Crystal Structure of the Lipase Lip_vut3 from Goat Rumen metagenome.

Components

Lip_vut3, C2L

Keywords

HYDROLASE / Lipase / goat rumen metagenomics

Function / homology

: / Hydrolases / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / sporulation resulting in formation of a cellular spore / hydrolase activity / FORMIC ACID / Spore germination lipase LipC

Function and homology information

Biological species

metagenome (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 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_vut3 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	Nov 13, 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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PDBx/mmCIF format	6nkd.cif.gz	184.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6nkd.ent.gz	150.9 KB	Display	PDB format
PDBx/mmJSON format	6nkd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6nkd_validation.pdf.gz	471.6 KB	Display	wwPDB validaton report
Full document	6nkd_full_validation.pdf.gz	475.2 KB	Display
Data in XML	6nkd_validation.xml.gz	17 KB	Display
Data in CIF	6nkd_validation.cif.gz	22.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nk/6nkd ftp://data.pdbj.org/pub/pdb/validation_reports/nk/6nkd	HTTPS FTP

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Related structure data

Similar structure data	6q1v-d 2ehj-d 1l1l-1 6rmc-1 4qdv-2 5osy-d 1st4-d 3bl7-d 3q1k-2 3q75-d 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_vut3, C2L

B: Lip_vut3, C2L

hetero molecules

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

1

A: Lip_vut3, C2L

B: Lip_vut3, C2L

hetero molecules

A: Lip_vut3, C2L

B: Lip_vut3, C2L

hetero molecules

defined by author&software
103 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.120, 93.120, 196.898
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

Components on special symmetry positions

ID	Model	Components
1	1	A-408- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Lip_vut3, C2L Mass: 25264.869 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: Q65NA4

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Non-polymers , 5 types, 31 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.47 Å³/Da / Density % sol: 50.12 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 2.40 M Ammonium Sulfate, 150 mM Formate pH 4.0, 3.0 % (v/v) 2-Butanol

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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: 2.8→50 Å / Num. obs: 13353 / % possible obs: 100 % / Redundancy: 29.2 % / B_iso Wilson estimate: 66.15 Å² / CC_1/2: 0.988 / R_merge(I) obs: 0.173 / Net I/σ(I): 32.9
Reflection shell	Resolution: 2.8→2.85 Å / Redundancy: 30.6 % / R_merge(I) obs: 0.879 / Num. unique obs: 654 / CC_1/2: 0.945 / % 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: 2.8→42.09 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.4

	R_factor	Num. reflection	% reflection
R_free	0.2565	701	5.27 %
R_work	0.2198	-	-
obs	0.2218	13298	99.78 %

Solvent computation

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

Displacement parameters

B_iso mean: 79.4 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→42.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3366	0	42	20	3428

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	3457
X-RAY DIFFRACTION	f_angle_d	0.469	4643
X-RAY DIFFRACTION	f_dihedral_angle_d	18.498	2103
X-RAY DIFFRACTION	f_chiral_restr	0.04	504
X-RAY DIFFRACTION	f_plane_restr	0.002	592

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 (%)
2.7857-3.0008	0.3553	130	0.3005	2442	X-RAY DIFFRACTION	99
3.0008-3.3027	0.3277	149	0.2688	2438	X-RAY DIFFRACTION	100
3.3027-3.7803	0.2751	141	0.2415	2471	X-RAY DIFFRACTION	100
3.7803-4.7617	0.2284	144	0.2048	2530	X-RAY DIFFRACTION	100
4.7617-42.095	0.2285	137	0.1942	2716	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	4.0772	2.2937	-0.7998	2.9556	-1.1864	4.3505	-0.3343	-0.4191	-0.2252	0.3129	-0.1416	0.0287	1.0782	0.0068	0.4971	0.8455	0.0482	0.0301	0.4346	-0.0397	0.6383	25.96	17.1423	34.0168
2	6.0081	2.1334	3.4441	5.1611	1.9254	5.6918	0.111	0.3527	-0.4519	-1.0535	0.1292	-0.5562	1.1068	1.8814	0.0412	0.7599	0.2451	0.1785	0.9286	-0.1777	0.6313	37.3403	12.8136	19.872
3	5.0875	-2.2671	2.4352	8.4731	1.6744	3.402	0.6936	-0.2012	-0.4843	0.6102	-0.574	-0.3831	2.2782	0.5062	0.0997	1.194	0.1974	-0.0799	0.5467	-0.0406	0.7666	31.6479	6.705	27.6617
4	3.4537	0.877	0.5861	8.0054	-4.683	8.5924	-0.1613	0.5136	-1.1295	-0.5999	0.4699	-0.4372	-0.0186	0.5914	-0.4348	0.5453	-0.0597	0.1431	0.9551	-0.0575	0.5681	34.2078	28.4977	5.3879
5	6.3672	3.4692	-1.4536	3.4172	-1.8199	1.022	-0.3661	0.8311	0.2444	-0.1496	0.8416	0.2111	1.8891	0.341	-0.2859	1.6812	0.1377	0.1241	0.2971	-0.2699	0.6553	29.6633	10.0275	12.5926
6	3.4691	-0.7742	-0.6246	4.9143	-1.4044	3.415	0.2566	0.507	-0.2611	0.3082	-0.1201	0.9141	1.2143	-0.4119	-0.0386	0.8903	-0.1519	-0.1035	0.5341	-0.0741	0.5601	20.9099	16.0931	16.0047
7	4.619	-2.2448	0.4352	1.5408	-0.0225	3.1615	-0.0411	0.1132	0.0798	0.0261	0.1287	0.303	0.5084	-0.3712	-0.1273	0.4892	-0.0649	-0.007	0.3165	-0.0086	0.4846	20.118	25.6988	25.3385
8	4.6125	0.1533	-0.194	1.7522	-0.8493	2.8645	0.0477	0.4411	-0.0651	0.0653	-0.0409	-0.5038	1.1816	0.9444	-0.1075	1.1717	0.4149	-0.0439	0.69	-0.109	0.4524	39.9485	10.9593	41.3613
9	4.2096	-0.7186	0.1187	2.1621	-0.69	4.7164	-0.0227	0.3517	0.1293	-0.3235	0.23	0.0068	0.5183	0.3072	-0.1853	0.682	0.2095	-0.0675	0.4702	0.0615	0.5563	35.2608	22.0627	45.3532
10	3.2768	0.9964	0.5652	5.3216	-0.6978	7.6774	0.0533	-0.9767	0.547	0.2382	0.0956	-0.3676	-0.5089	1.2529	-0.1267	0.796	0.1477	-0.0052	1.0276	-0.0847	0.7939	61.4031	31.9925	43.6368
11	9.4492	4.6389	1.184	2.47	0.6208	4.603	-0.1188	-0.0748	0.5462	1.1613	0.27	0.1644	-0.0889	-0.0454	-0.1824	0.8142	0.2066	-0.0199	0.5503	-0.0383	0.7509	39.9836	27.5033	54.7179
12	5.1617	0.1412	-0.5512	2.358	0.5283	3.3354	-0.1891	-0.3759	-0.2766	0.4179	0.1554	-0.5398	0.9977	0.8782	-0.1589	0.8592	0.3354	-0.0539	0.7781	-0.018	0.6111	50.0081	19.0873	53.8306
13	4.3935	-0.0601	0.0969	2.8965	-0.0535	3.7054	-0.5384	0.1348	-0.3328	0.5133	0.5934	-0.5867	1.1962	1.1219	-0.0658	0.9797	0.4677	-0.0752	0.918	-0.1206	0.6198	51.3062	9.6179	44.6033

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 47 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 48 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 80 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 81 through 97 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 98 through 122 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 123 through 170 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 171 through 211 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 37 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 38 through 80 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 81 through 105 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 106 through 122 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 123 through 170 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 171 through 211 )

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