PDB-8qdr: Vitis vinifera dimeric 13S-lipoxygenase LOXA in a detergent bound...

ID or keywords:

Entry

Database: PDB / ID: 8qdr

Title

Vitis vinifera dimeric 13S-lipoxygenase LOXA in a detergent bound open conformation

Components

Lipoxygenase

Keywords

OXIDOREDUCTASE / Vitis vinifera / 13S-lipoxygenase / allostery / dimeric enzyme / non-heme-iron / membrane-activated enzyme

Function / homology

Function and homology information

Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Vitis vinifera (wine grape)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Wild, K. / Sinning, I.

Funding support

Germany, 1items

Citation

Journal: J.Mol.Biol. / Year: 2024
Title: Vitis vinifera Lipoxygenase LoxA is an Allosteric Dimer Activated by Lipidic Surfaces.
Authors: Pilati, S. / Wild, K. / Gumiero, A. / Holdermann, I. / Hackmann, Y. / Serra, M.D. / Guella, G. / Moser, C. / Sinning, I.

History

Deposition	Aug 30, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 30, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8qdr.cif.gz	599 KB	Display	PDBx/mmCIF format
PDB format	pdb8qdr.ent.gz	484 KB	Display	PDB format
PDBx/mmJSON format	8qdr.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/qd/8qdr ftp://data.pdbj.org/pub/pdb/validation_reports/qd/8qdr	HTTPS FTP

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Related structure data

Related structure data	8qdqC C: citing same article (ref.)
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: Lipoxygenase

B: Lipoxygenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	85.905, 105.818, 88.533
Angle α, β, γ (deg.)	90.00, 92.84, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lipoxygenase Mass: 97448.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VIT_06s0004g01510 / Production host: Escherichia coli (E. coli) / References: UniProt: D7SLA9
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PQE / 3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL / ANAPOE-C12E8 Mass: 536.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₉H₆₀O₈
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.35 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 9.2, 26.4% PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2→45.2 Å / Num. obs: 106427 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC_1/2: 0.996 / R_pim(I) all: 0.067 / Net I/σ(I): 9
Reflection shell	Resolution: 2→2.07 Å / Num. unique obs: 10568 / R_pim(I) all: 0.605 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→40.795 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2179	5301	4.98 %
R_work	0.1738	-	-
obs	0.176	106409	99.76 %

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→40.795 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11355	0	46	669	12070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	11742
X-RAY DIFFRACTION	f_angle_d	0.825	15956
X-RAY DIFFRACTION	f_dihedral_angle_d	13.43	7020
X-RAY DIFFRACTION	f_chiral_restr	0.05	1720
X-RAY DIFFRACTION	f_plane_restr	0.006	2047

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 (%)
2-2.0227	0.3347	148	0.2874	3338	X-RAY DIFFRACTION	100
2.0227-2.0465	0.3349	167	0.2908	3375	X-RAY DIFFRACTION	100
2.0465-2.0715	0.3228	181	0.2803	3354	X-RAY DIFFRACTION	100
2.0715-2.0977	0.2925	166	0.2651	3386	X-RAY DIFFRACTION	100
2.0977-2.1253	0.2988	176	0.2599	3347	X-RAY DIFFRACTION	100
2.1253-2.1544	0.2933	188	0.2483	3351	X-RAY DIFFRACTION	100
2.1544-2.1852	0.3018	183	0.2379	3299	X-RAY DIFFRACTION	100
2.1852-2.2178	0.2623	188	0.2257	3413	X-RAY DIFFRACTION	100
2.2178-2.2525	0.2728	196	0.2275	3314	X-RAY DIFFRACTION	100
2.2525-2.2894	0.2608	169	0.212	3352	X-RAY DIFFRACTION	100
2.2894-2.3289	0.2504	169	0.2048	3364	X-RAY DIFFRACTION	100
2.3289-2.3712	0.2472	191	0.2053	3349	X-RAY DIFFRACTION	100
2.3712-2.4168	0.2511	173	0.1961	3366	X-RAY DIFFRACTION	100
2.4168-2.4661	0.2613	167	0.1893	3405	X-RAY DIFFRACTION	100
2.4661-2.5197	0.2229	172	0.1858	3369	X-RAY DIFFRACTION	100
2.5197-2.5783	0.2306	205	0.1834	3336	X-RAY DIFFRACTION	100
2.5783-2.6428	0.239	172	0.1808	3335	X-RAY DIFFRACTION	100
2.6428-2.7143	0.2232	209	0.1806	3351	X-RAY DIFFRACTION	100
2.7143-2.7941	0.2271	187	0.17	3358	X-RAY DIFFRACTION	100
2.7941-2.8843	0.2368	155	0.1721	3390	X-RAY DIFFRACTION	100
2.8843-2.9873	0.2415	157	0.1715	3365	X-RAY DIFFRACTION	100
2.9873-3.1069	0.2254	179	0.1688	3392	X-RAY DIFFRACTION	100
3.1069-3.2482	0.2244	215	0.1613	3341	X-RAY DIFFRACTION	100
3.2482-3.4194	0.1941	182	0.1533	3373	X-RAY DIFFRACTION	100
3.4194-3.6335	0.1806	159	0.1494	3402	X-RAY DIFFRACTION	100
3.6335-3.9139	0.1847	199	0.1379	3364	X-RAY DIFFRACTION	100
3.9139-4.3074	0.1702	162	0.1333	3412	X-RAY DIFFRACTION	100
4.3074-4.9297	0.1585	147	0.1287	3421	X-RAY DIFFRACTION	100
4.9297-6.2074	0.1969	158	0.1568	3422	X-RAY DIFFRACTION	100
6.2074-40.795	0.1786	181	0.1649	3464	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	1.2484	0.1504	-0.5592	2.4784	-0.7405	1.4906	-0.0469	-0.3228	-0.3141	0.3029	-0.0361	-0.3679	0.3501	0.2491	0.0833	0.3791	0.0458	-0.0785	0.2744	0.0323	0.4044	138.066	62.9685	96.781
2	1.119	-0.5743	-0.1467	1.3666	0.7867	0.8407	0.005	0.1157	-0.3842	-0.0342	-0.1303	0.3094	0.1128	-0.1867	0.1168	0.2623	-0.0196	-0.0176	0.1894	0.0049	0.2738	107.506	71.855	86.9684
3	1.7286	-0.4519	-0.4552	0.6418	0.3573	0.3184	0.0493	0.146	0.0021	-0.0722	-0.0745	0.072	-0.0015	-0.1224	0.026	0.218	0.003	-0.0115	0.1985	0.0166	0.1577	101.5194	91.165	91.7879
4	3.532	0.63	-2.1906	1.6081	0.2045	1.5371	0.0175	-0.2699	-0.7224	0.088	-0.1232	0.2894	0.1522	-0.1808	0.0875	0.2793	-0.0281	0.04	0.3425	-0.0522	0.3227	80.3131	84.6455	99.2905
5	2.2112	0.4297	0.5025	0.2174	0.0727	0.1504	0.2581	-0.5317	-0.8316	0.0897	-0.0854	-0.0616	0.0837	-0.0234	-0.1656	0.3609	0.0164	-0.0069	0.2585	0.0234	0.4813	100.6478	77.9629	104.6949
6	3.9434	0.0216	-0.0334	0.1888	-0.2449	1.1037	-0.1113	-0.2736	-0.4253	0.0625	0.0963	0.0903	0.123	-0.1193	-0.0146	0.2185	-0.0235	0.0011	0.2651	-0.0043	0.2281	113.2902	91.6621	110.8142
7	1.8081	0.7293	-0.079	1.846	-0.7871	2.2277	0.0234	0.015	-0.2591	-0.0513	0.0914	0.2003	0.3607	-0.2288	-0.1152	0.2789	-0.03	0.0345	0.2394	-0.0313	0.2052	27.2148	86.9048	148.7637
8	0.7007	0.4258	-0.6674	0.3784	-0.5878	1.4626	0.0169	-0.4917	-0.0899	0.126	-0.1175	-0.0831	0.0136	0.6397	0.0628	0.2476	0.0088	-0.0343	0.4998	0.0364	0.2456	61.6512	96.9565	145.1914
9	1.4634	0.0084	0.0156	0.9068	-0.3801	2.6118	0.0237	-0.3605	0.2643	0.0785	-0.1164	-0.1217	-0.3706	0.321	0.087	0.2135	-0.0524	0.0104	0.2927	-0.0318	0.2185	74.159	112.4332	124.4471
10	1.5526	0.023	-0.9267	0.1761	-0.0961	0.9816	0.0142	-0.3222	-0.0198	0.0666	-0.0257	-0.0613	-0.0458	0.3384	0.0155	0.2043	-0.0044	-0.0097	0.2855	-0.0086	0.1629	63.1032	102.3971	133.9627
11	2.1355	-0.0185	-1.3156	0.7421	0.1376	1.4844	0.0941	0.0698	0.1404	0.0974	-0.0013	0.0194	-0.1689	-0.0029	-0.0963	0.2464	0.024	0.0066	0.1889	0.0079	0.2075	43.5166	108.568	130.0004
12	5.2736	0.0182	-0.1527	0.496	-0.0704	0.6969	-0.0489	-0.282	-0.6262	0.0319	-0.0039	-0.119	0.1629	0.2412	0.0303	0.3389	0.0255	0.0096	0.46	0.0759	0.2578	72.5107	92.1887	130.1678
13	3.6485	-0.3176	-0.5484	0.7618	0.6548	0.7138	-0.1123	-0.0716	-0.3457	0.0204	-0.0003	0.0008	0.0386	-0.0819	0.0804	0.2032	0.0187	-0.0232	0.2949	0.0021	0.2069	48.51	94.1543	116.3355

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 66 through 214 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 215 through 411 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 412 through 747 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 748 through 791 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 792 through 838 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 839 through 901 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 67 through 249 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 250 through 411 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 412 through 504 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 505 through 654 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 655 through 754 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 755 through 838 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 839 through 901 )

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