PDB-4wha: Lipoxygenase-1 (soybean) L546A/L754A mutant

ID or keywords:

Entry

Database: PDB / ID: 4wha

Title

Lipoxygenase-1 (soybean) L546A/L754A mutant

Components

Seed linoleate 13S-lipoxygenase-1

Keywords

OXIDOREDUCTASE / lipoxygenase / tunneling / C-H activation

Function / homology

Function and homology information

linolenate 9R-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / oxylipin biosynthetic process / fatty acid oxidation / iron ion binding / cytoplasm
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Scouras, A.D. / Carr, C.A.M. / Hu, S. / Klinman, J.P.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM025765	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P50GM082250	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	T32GM008295	United States

Citation

Journal: J.Am.Chem.Soc. / Year: 2014
Title: Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation.
Authors: Hu, S. / Sharma, S.C. / Scouras, A.D. / Soudackov, A.V. / Carr, C.A. / Hammes-Schiffer, S. / Alber, T. / Klinman, J.P.

History

Deposition	Sep 21, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 19, 2014	Group: Other
Revision 1.2	Aug 23, 2017	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.version
Revision 1.3	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4wha.cif.gz	545.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4wha.ent.gz	457.8 KB	Display	PDB format
PDBx/mmJSON format	4wha.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wh/4wha ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4wha	HTTPS FTP

-
Related structure data

Related structure data	3pzwS S: Starting model for refinement
Similar structure data	2iuj-d 3bne-d 5t5v-1 3pzw-d 1yge-d 5hqm-d 5tqn-2 5t5v-2 2cwx-d 1fgr-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Seed linoleate 13S-lipoxygenase-1

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	94.126, 92.644, 49.572
Angle α, β, γ (deg.)	90.00, 90.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Seed linoleate 13S-lipoxygenase-1 / Lipoxygenase-1 / L-1 Mass: 94438.000 Da / Num. of mol.: 1 / Mutation: L546A, L754A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Tissue: seedling / Gene: LOX1.1, LOX1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P08170, linoleate 13S-lipoxygenase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1017 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.26 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 9% PEG3350, 200 mM sodium acetate, pH 5.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.116 Å / Relative weight: 1
Reflection	Resolution: 1.7→66.03 Å / Num. obs: 28667 / % possible obs: 99.8 % / Redundancy: 5.5 % / R_sym value: 0.111 / Net I/σ(I): 10.09
Reflection shell	Resolution: 1.7→1.761 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PZW

3pzw

Resolution: 1.7→66.026 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1789	2504	2.69 %
R_work	0.1373	-	-
obs	0.1384	28667	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→66.026 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6548	0	61	1017	7626

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7414
X-RAY DIFFRACTION	f_angle_d	0.891	10115
X-RAY DIFFRACTION	f_dihedral_angle_d	13.18	2821
X-RAY DIFFRACTION	f_chiral_restr	0.049	1081
X-RAY DIFFRACTION	f_plane_restr	0.007	1344

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 (%)
1.7-1.7327	0.3218	141	0.2671	4978	X-RAY DIFFRACTION	100
1.7327-1.7681	0.2998	144	0.2454	5058	X-RAY DIFFRACTION	100
1.7681-1.8065	0.2506	144	0.2178	4995	X-RAY DIFFRACTION	100
1.8065-1.8485	0.2701	130	0.1983	4995	X-RAY DIFFRACTION	100
1.8485-1.8948	0.2062	141	0.1808	5030	X-RAY DIFFRACTION	100
1.8948-1.946	0.2261	140	0.1742	5039	X-RAY DIFFRACTION	100
1.946-2.0033	0.2161	131	0.1699	5025	X-RAY DIFFRACTION	100
2.0033-2.0679	0.2059	137	0.1523	5053	X-RAY DIFFRACTION	100
2.0679-2.1419	0.1752	136	0.1439	5023	X-RAY DIFFRACTION	100
2.1419-2.2276	0.1857	139	0.1342	5013	X-RAY DIFFRACTION	100
2.2276-2.329	0.1765	145	0.1285	5036	X-RAY DIFFRACTION	100
2.329-2.4518	0.158	133	0.1203	5050	X-RAY DIFFRACTION	100
2.4518-2.6054	0.1535	146	0.1171	5056	X-RAY DIFFRACTION	100
2.6054-2.8066	0.182	133	0.1229	5040	X-RAY DIFFRACTION	100
2.8066-3.089	0.1602	141	0.1269	5068	X-RAY DIFFRACTION	100
3.089-3.536	0.1699	136	0.1239	5043	X-RAY DIFFRACTION	99
3.536-4.4548	0.1381	140	0.1137	5062	X-RAY DIFFRACTION	100
4.4548-66.0763	0.1803	147	0.1321	5152	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	0.2925	-0.3516	0.0151	0.4564	0.0264	0.2027	-0.0597	0.2056	-0.0287	-0.0421	-0.0236	-0.0973	-0.1441	0.2216	-0.0011	0.3133	0.0337	0.1805	0.494	-0.0321	0.8411	59.8523	42.9976	0.9862
2	0.0035	-0.0032	-0.0044	0.0112	-0.0028	0.0106	-0.0121	0.0287	-0.017	-0.168	0.0789	-0.0031	-0.149	0.0993	0	0.3859	-0.0334	0.1473	0.478	0.1221	0.8506	55.8862	54.6157	-1.1402
3	0.1013	0.1172	0.0026	0.2175	0.0535	0.0405	0.0461	0.0292	-0.1069	0.026	-0.1117	-0.618	0.0135	0.2491	0.1074	0.2332	0.025	0.0899	0.4346	0.0911	0.9246	64.7664	40.8241	9.76
4	0.5478	-0.2326	0.0507	0.2265	-0.0506	0.0469	0.0013	-0.0794	-0.1728	-0.0253	-0.0295	-0.7336	0.035	0.1482	0.0305	0.2579	0.0149	0.0026	0.3453	0.0123	0.828	57.4736	40.484	13.1047
5	0.4213	-0.019	-0.1659	0.3881	-0.1966	0.1985	0.1406	-0.3562	0.2254	0.2516	-0.0101	-0.3504	-0.1304	0.1227	0.016	0.2845	-0.0351	-0.0663	0.2914	-0.0418	0.3435	33.3045	55.7924	24.6216
6	0.0114	0.0066	0.0078	0.0005	0.0021	0.0033	-0.1292	-0.0414	0.1262	-0.1019	-0.1122	-0.2437	-0.1041	0.1419	-0.0001	0.229	-0.0064	0.0556	0.2884	0.0189	0.4016	35.4033	50.9146	1.7296
7	0.0751	0.0063	-0.1	0.0087	-0.0308	0.1194	0.1974	-0.1684	0.4604	0.0563	-0.1116	-0.212	-0.3493	-0.0116	0.0086	0.3042	-0.0414	0.0061	0.2355	0.0069	0.3159	15.9784	65.0403	4.5837
8	0.5821	-0.1277	-0.0168	0.8713	-0.0978	0.1153	-0.0118	0.2194	0.0406	-0.1867	-0.017	-0.2455	0.0154	-0.084	-0.0273	0.1897	0.0088	0.0306	0.1952	0.0309	0.0883	12.7224	52.6863	-3.0204
9	0.1614	-0.0492	-0.0065	0.0318	0.0507	0.0481	0.0234	-0.2342	-0.0367	0.3016	-0.0853	0.0576	-0.0026	-0.0357	-0.1192	0.382	-0.0567	0.0126	0.2945	0.0094	0.1092	0.0886	36.5654	29.1016
10	0.4727	-0.0511	-0.1104	0.4387	-0.2055	0.579	0.0712	-0.209	-0.0713	0.3936	-0.0782	0.3166	-0.0442	-0.1501	0.5921	0.2502	-0.0334	0.0717	0.179	-0.0479	-0.0265	-1.8452	39.8333	19.9144
11	0.0021	-0.003	-0.0048	0.0115	-0.0008	0.0068	-0.0128	0.2444	0.1639	-0.1576	-0.0909	0.3285	0.0935	-0.097	0.0001	0.1858	0.0025	-0.0421	0.2926	-0.0007	0.17	-11.3828	43.7448	7.6176
12	0.607	0.2548	0.0052	0.534	-0.0755	0.3513	0.034	-0.1403	-0.0391	0.1046	-0.0539	-0.2616	-0.0027	0.0125	-0.0678	0.1607	-0.0033	-0.0434	0.1483	0.0183	0.1616	22.5495	43.0111	18.088
13	0.4984	-0.0855	-0.267	0.0353	0.0234	0.1705	-0.2427	0.0731	-0.274	-0.1064	-0.0477	-0.2621	0.1288	0.0361	-0.0077	0.3567	0.0101	0.02	0.1964	0.0944	0.5642	15.6648	15.5301	15.5218
14	0.525	-0.1895	0.1789	0.2023	0.0303	1.0733	-0.0427	0.0009	-0.5389	0.0239	-0.0902	-0.5095	0.2724	-0.1008	-0.7836	0.2473	0.0305	-0.0461	0.0529	0.118	0.6062	29.1503	22.3997	14.6089
15	0.0115	-0.0175	0.033	0.0121	-0.0281	0.138	0.0576	-0.4744	-0.2455	0.3667	-0.0874	-0.3684	0.1039	0.0574	-0.1331	0.3288	-0.013	-0.18	0.4065	0.1672	0.437	34.7184	32.9327	30.912
16	0.5058	0.3684	-0.1278	0.3173	0.0363	0.1661	0.0291	-0.0667	-0.2147	0.0428	-0.0422	-0.2597	0.0404	0.0153	-0.0179	0.1899	0.007	-0.0238	0.1586	0.0275	0.219	21.8565	36.654	13.4627
17	0.0912	0.1988	-0.0445	0.4446	-0.1065	0.0298	0.0828	0.0744	0.3054	0.1674	0.1218	0.4639	-0.2012	-0.3619	0.0505	0.1461	0.0737	0.0495	0.3045	0.0516	0.2279	-8.8704	56.4465	9.4878
18	0.1855	-0.0786	-0.1094	0.534	0.0127	0.1299	-0.0704	0.041	0.0213	0.0088	0.0405	-0.2661	0.0098	-0.0338	-0.0215	0.1346	0.0196	0.0396	0.1269	0.0086	0.1553	22.0898	47.9998	4.0229
19	0.1765	0.0181	-0.2915	0.0038	-0.0524	0.4799	0.0698	0.2601	-0.2813	-0.131	-0.0864	-0.403	0.2146	0.1032	-0.031	0.2883	0.0454	0.0844	0.2282	-0.064	0.6382	36.0477	23.9836	2.5398
20	0.5239	0.2668	0.0148	0.9553	-0.1017	0.1294	-0.0358	0.1916	-0.2363	-0.1765	-0.0049	-0.3346	0.1073	0.0332	-0.0773	0.2112	-0.004	0.0531	0.1955	-0.0413	0.1835	17.8077	33.2168	-0.568

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 6:20)
2	X-RAY DIFFRACTION	2	(chain A and resid 21:37)
3	X-RAY DIFFRACTION	3	(chain A and resid 38:74)
4	X-RAY DIFFRACTION	4	(chain A and resid 75:170)
5	X-RAY DIFFRACTION	5	(chain A and resid 171:245)
6	X-RAY DIFFRACTION	6	(chain A and resid 246:258)
7	X-RAY DIFFRACTION	7	(chain A and resid 259:284)
8	X-RAY DIFFRACTION	8	(chain A and resid 285:359)
9	X-RAY DIFFRACTION	9	(chain A and resid 360:380)
10	X-RAY DIFFRACTION	10	(chain A and resid 381:466)
11	X-RAY DIFFRACTION	11	(chain A and resid 467:478)
12	X-RAY DIFFRACTION	12	(chain A and resid 479:591)
13	X-RAY DIFFRACTION	13	(chain A and resid 592:602)
14	X-RAY DIFFRACTION	14	(chain A and resid 603:639)
15	X-RAY DIFFRACTION	15	(chain A and resid 640:667)
16	X-RAY DIFFRACTION	16	(chain A and resid 668:712)
17	X-RAY DIFFRACTION	17	(chain A and resid 713:736)
18	X-RAY DIFFRACTION	18	(chain A and resid 737:767)
19	X-RAY DIFFRACTION	19	(chain A and resid 768:798)
20	X-RAY DIFFRACTION	20	(chain A and resid 799:839)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi