PDB-6ns5: Crystal structure of fungal lipoxygenase from Fusarium graminearu...

ID or keywords:

Entry

Database: PDB / ID: 6ns5

Title

Crystal structure of fungal lipoxygenase from Fusarium graminearum. Second C2 crystal form.

Components

lipoxygenase

Keywords

OXIDOREDUCTASE / lipoxygenase / fungus / Fe coordination

Function / homology

Function and homology information

linoleate 11-lipoxygenase / linoleate 11-lipoxygenase activity / lipid oxidation / linoleic acid metabolic process / metal ion binding
Similarity search - Function

Biological species

Gibberella zeae (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.79 Å

Authors

Pakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	HL 107887	United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	RR-15301	United States

Citation

Journal: Protein Sci. / Year: 2019
Title: An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere.
Authors: Pakhomova, S. / Boeglin, W.E. / Neau, D.B. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.

History

Deposition	Jan 24, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ns5.cif.gz	535.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6ns5.ent.gz	439.1 KB	Display	PDB format
PDBx/mmJSON format	6ns5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ns5_validation.pdf.gz	442.5 KB	Display	wwPDB validaton report
Full document	6ns5_full_validation.pdf.gz	453.2 KB	Display
Data in XML	6ns5_validation.xml.gz	44.6 KB	Display
Data in CIF	6ns5_validation.cif.gz	61.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ns/6ns5 ftp://data.pdbj.org/pub/pdb/validation_reports/ns/6ns5	HTTPS FTP

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Related structure data

Related structure data	6ns2C 6ns3C 6ns4C 6ns6C 3rdeS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6ns4-d 6ns6-d 6d50-d 6iwq-3 3dpm-d 5of0-1 1n9e-1 5uj6-d 3fip-d 3ad7-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

Deposited unit

A: lipoxygenase

B: lipoxygenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	123.365, 113.671, 99.437
Angle α, β, γ (deg.)	90.00, 90.25, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 9 - 736 / Label seq-ID: 33 - 760

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

#1: Protein	lipoxygenase Mass: 86406.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus) Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FG02216.1, FGRAMPH1_01T05341 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: I1REW2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical	ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: 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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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.05 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 22% PEG3350, 0.3 M ammonium acetate, 0.1 M Tris

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2016 / Details: MIRRORS

Radiation

Monochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.814
1	1	h,-k,-l	2	0.186

Reflection

Resolution: 2.79→83.59 Å / Num. obs: 33864 / % possible obs: 100 % / Redundancy: 3.8 % / B_iso Wilson estimate: 41.7 Å² / CC_1/2: 0.992 / R_pim(I) all: 0.076 / Net I/σ(I): 8.6

Reflection shell

Resolution: 2.79→2.94 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4463 / CC_1/2: 0.581 / R_pim(I) all: 0.428 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3RDE

3rde

Resolution: 2.79→64.08 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.877 / SU B: 24.908 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2372	1089	3.2 %	RANDOM
R_work	0.17481	-	-	-
obs	0.1768	32762	98.77 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 47.232 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-25.46 Å²	-0 Å²	-1.88 Å²
2-	-	-23.98 Å²	-0 Å²
3-	-	-	49.44 Å²

Refinement step

Cycle: 1 / Resolution: 2.79→64.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10587	0	2	20	10609

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	10862
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	10206
X-RAY DIFFRACTION	r_angle_refined_deg	1.528	1.953	14746
X-RAY DIFFRACTION	r_angle_other_deg	1.031	3	23568
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.469	5	1328
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.676	24.95	499
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.35	15	1813
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.73	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1625
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	12230
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	2426
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.848	1.586	5342
X-RAY DIFFRACTION	r_mcbond_other	0.848	1.586	5341
X-RAY DIFFRACTION	r_mcangle_it	1.476	2.374	6660
X-RAY DIFFRACTION	r_mcangle_other	1.476	2.375	6661
X-RAY DIFFRACTION	r_scbond_it	0.767	1.603	5520
X-RAY DIFFRACTION	r_scbond_other	0.767	1.603	5520
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.218	2.379	8087
X-RAY DIFFRACTION	r_long_range_B_refined	2.498	12.31	12475
X-RAY DIFFRACTION	r_long_range_B_other	2.495	12.31	12475
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 39494 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.789→2.861 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.298	56	-
R_work	0.233	2028	-
obs	-	-	83.49 %

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	4.8574	0.0317	2.3141	2.2169	-0.5631	3.2044	-0.0278	0.1153	-0.1374	-0.1222	-0.0178	0.2182	0.1646	-0.0505	0.0456	0.4615	0.039	0.1553	0.3038	-0.0267	0.1961	34.132	-21.953	21.823
2	2.0116	-1.3637	1.2107	2.5827	-0.309	1.0046	0.0957	0.1686	-0.0342	-0.48	-0.0254	-0.3698	0.0566	-0.047	-0.0703	0.4044	-0.0092	0.1775	0.5329	-0.1182	0.1335	20.658	-0.937	7.152
3	2.491	-0.2164	-1.0457	2.4383	-0.1057	4.4443	-0.0895	-0.0127	-0.0781	-0.1537	0.1456	-0.1591	-0.0853	0.4172	-0.0562	0.3407	0.0108	-0.0196	0.3775	-0.0277	0.2574	14.833	-17.822	31.869
4	1.1962	0.2925	-0.4436	1.2256	-0.638	1.5303	0.031	0.1343	-0.1233	-0.0292	0.0046	0.1916	0.1012	-0.2017	-0.0356	0.3292	0.0032	0.0069	0.303	-0.0161	0.0565	-2.486	-3.758	25.387
5	1.159	0.3836	-0.1329	1.5901	-1.2306	2.4749	0.0045	0.1593	0.0513	0.1366	0.029	-0.0236	-0.1566	-0.2098	-0.0336	0.2701	0.0679	0.026	0.3023	0.0331	0.0093	4.4	15.306	17.263
6	3.9333	-1.7258	0.7083	1.8996	0.9191	2.1552	-0.1181	0.0547	-0.3185	-0.1682	0.1227	-0.0268	0.1599	0.1406	-0.0047	0.4026	-0.001	0.106	0.2278	-0.0505	0.1774	3.527	-15.071	29.435
7	7.0327	-0.3535	-2.1295	3.3477	0.8609	7.3768	0.0387	0.3223	0.6695	-0.3136	-0.0241	-0.1089	-0.4644	0.3235	-0.0146	0.4127	0.0112	0.0224	0.345	-0.0067	0.1181	23.83	24.299	23.928
8	1.9068	4.5584	0.3047	10.9221	0.7165	0.0675	0.1423	-0.0678	-0.1476	0.3109	-0.1682	-0.4269	-0.0015	0.0618	0.0259	0.2904	-0.0411	0.0087	0.4528	0.0777	0.2408	9.901	10.963	39.247
9	4.2034	-0.0724	-2.0649	2.4471	0.5341	3.1851	0.0143	0.1792	0.0469	-0.1291	0.0746	-0.2103	0.0628	0.0301	-0.0888	0.375	0.04	-0.0574	0.2659	0.0699	0.1255	24.986	19.667	18.735
10	2.652	-1.9673	-0.0366	1.685	0.2332	1.7555	0.0168	0.1569	0.0964	-0.169	-0.0891	0.1142	-0.1765	0.0026	0.0722	0.3658	0.0289	-0.0336	0.3681	0.0395	0.1947	40.219	-1.045	7.912
11	2.4043	0.0585	1.5827	0.9003	0.5525	3.7506	-0.1642	-0.1213	0.006	-0.1659	0.1567	0.1677	0.0482	-0.5097	0.0075	0.562	0.0101	0.017	0.4905	-0.0648	0.2555	46.141	15.121	25.934
12	1.6721	0.3785	0.1185	1.9299	0.4281	1.0101	0.002	-0.1688	0.1938	0.1115	0.0538	-0.307	-0.11	0.2309	-0.0558	0.3668	0.0386	0.0338	0.3962	-0.0532	0.1011	63.896	2.59	24.151
13	1.5388	0.6926	0.2036	1.947	0.4709	1.4249	-0.0026	-0.1506	-0.0344	0.1092	0.0722	-0.1561	0.0964	0.1531	-0.0696	0.3257	0.0795	0.0233	0.3215	-0.0083	0.0175	56.372	-17.176	19.995
14	4.701	-0.3395	-0.1293	2.7297	-0.4306	2.6592	-0.1215	0.045	0.189	-0.1341	0.1405	-0.0421	-0.3269	-0.0215	-0.019	0.3915	0.0077	0.0313	0.2999	-0.0965	0.0855	58.523	15.557	26.501
15	6.6391	-1.2767	1.0755	3.6547	-1.2642	2.4888	0.0425	-0.0146	-0.0896	0.0736	-0.104	0.4779	0.1163	-0.1683	0.0615	0.403	0.041	0.0888	0.4319	0.0421	0.1097	39.082	-21.658	30.52
16	3.8166	-4.4366	1.8948	8.073	-6.6779	7.8662	-0.039	-0.4944	-0.1429	-0.3068	0.3611	0.3636	0.5571	-0.108	-0.3221	0.3644	-0.0183	0.1173	0.7386	-0.1075	0.1951	52.137	-6.665	40.841

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 71
2	X-RAY DIFFRACTION	2	A	72 - 172
3	X-RAY DIFFRACTION	3	A	173 - 230
4	X-RAY DIFFRACTION	4	A	231 - 470
5	X-RAY DIFFRACTION	5	A	471 - 600
6	X-RAY DIFFRACTION	6	A	601 - 670
7	X-RAY DIFFRACTION	7	A	671 - 711
8	X-RAY DIFFRACTION	8	A	712 - 737
9	X-RAY DIFFRACTION	9	B	8 - 66
10	X-RAY DIFFRACTION	10	B	67 - 133
11	X-RAY DIFFRACTION	11	B	134 - 236
12	X-RAY DIFFRACTION	12	B	237 - 470
13	X-RAY DIFFRACTION	13	B	471 - 600
14	X-RAY DIFFRACTION	14	B	601 - 662
15	X-RAY DIFFRACTION	15	B	663 - 718
16	X-RAY DIFFRACTION	16	B	719 - 737

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