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- PDB-1ik3: LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E... -

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Basic information

Entry
Database: PDB / ID: 1ik3
TitleLIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID
ComponentsLIPOXYGENASE-3
KeywordsOXIDOREDUCTASE / PURPLE LIPOXYGENASE / FE(III) COMPLEX / INTERM
Function / homology
Function and homology information


linoleate 9S-lipoxygenase / linoleate 9S-lipoxygenase activity / 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 / cytoplasm
Similarity search - Function
Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 ...Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase-1 / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Nuclear Transport Factor 2; Chain: A, / Few Secondary Structures / Irregular / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-11O / 13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID / 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID / Chem-9OH / : / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSkrzypczak-Jankun, E. / Funk Jr., M.O.
Citation
Journal: J.Am.Chem.Soc. / Year: 2001
Title: Three-dimensional structure of a purple lipoxygenase.
Authors: Skrzypczak-Jankun, E. / Bross, R.A. / Carroll, R.T. / Dunham, W.R. / Funk, M.O.
#1: Journal: Proteins / Year: 1997
Title: Structure of Soybean Lipoxygenase L3 and a Comparison with its L1 Isoenzyme
Authors: Skrzypczak-Jankun, E. / Amzel, L.M. / Kroa, B.A. / Funk Jr., M.O.
#2: Journal: Biochemistry / Year: 1998
Title: Structural and Thermochemical Characterization of Lipoxygenase-Catechol Complexes
Authors: Pham, C. / Jankun, J. / Skrzypczak-Jankun, E. / Flowers II, R.A. / Funk Jr., M.O.
#3: Journal: INT.J.MOL.MED. / Year: 2000
Title: Curcumin Inhibits Lipoxygenase by Binding to its Central Cavity: Theoretical and X-Ray Evidence.
Authors: Skrzypczak-Jankun, E. / Mccabe, N.P. / Selman, S.H. / Jankun, J.
History
DepositionMay 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPOXYGENASE-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2256
Polymers96,9191
Non-polymers1,3065
Water9,530529
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.650, 137.280, 61.890
Angle α, β, γ (deg.)90.00, 95.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1325-

HOH

21A-1389-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LIPOXYGENASE-3 /


Mass: 96919.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Strain: PROVAR CULTIVAR / References: UniProt: P09186, linoleate 13S-lipoxygenase

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Non-polymers , 6 types, 534 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-13S / 13(S)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID


Mass: 312.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O4
#4: Chemical ChemComp-13R / 13(R)-HYDROPEROXY-9(Z),11(E)-OCTADECADIENOIC ACID


Mass: 312.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O4
#5: Chemical ChemComp-9OH / (TRANS-12,13-EPOXY)-9-HYDROXY-10(E)-OCTADECENOIC ACID


Mass: 312.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O4
#6: Chemical ChemComp-11O / (TRANS-12,13-EPOXY)-11-HYDROXY-9(Z)-OCTADECENOIC ACID


Mass: 312.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: PEG 8000, citrate-phosphate buffer, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃
Details: drop1:drop2:drop3:drop4=3:6:1:2ratio, Skrzypczak-Jankun, E., (1997) Proteins: Struct.,Funct., Genet., 29, 15.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlL31drop1
20.1 MTris-HCl1drop1pH7.0
320 %(w/v)PEG80001drop2
40.05 Msodium citrate phosphate1drop2pH4.6
50.2 %(w/v)1drop2NaN3
60.1 Msodium phosphate1drop3pH7.0
820 %PEG80001reservoir
7water1drop4

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 48693 / Num. obs: 41035 / % possible obs: 78 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 1.3 / % possible all: 68
Reflection
*PLUS
% possible obs: 78 % / Num. measured all: 107634
Reflection shell
*PLUS
% possible obs: 68 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LNH, PROTEIN ONLY

1lnh


Resolution: 2→40 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: DISORDERED REGIONS 1-8 AND 33-45 WERE OMITTED FROM CALCULATIONS. There are four ligands in the coordinate section: 13S, 13R, 9OH, and 11O. 13S is alternate conformation A, occupancy 1.00. ...Details: DISORDERED REGIONS 1-8 AND 33-45 WERE OMITTED FROM CALCULATIONS. There are four ligands in the coordinate section: 13S, 13R, 9OH, and 11O. 13S is alternate conformation A, occupancy 1.00. 13R is alternate conformation B, occupancy 0.00. 9OH is alternate conformation C, occupancy 0.00. 11O is alternate conformation D, occupancy 0.00. The author refined both R and S conformations of the 13-hydroperoxy-9(Z),11(E)-octadecadienoic acid and the S came with lower discrepancy factor. Also in the soaking solution S was present as 86% versus only 14% of R. However it DOES NOT mean that the occupancy was 0.86 and 0.14 because lipoxygenase isozyme L3 turns 60% of R and 40% of S in its catalytic reaction, so it is difficult to judge what was the REAL occupancy for these two 13-S,R-isomers, because of the enzyme different affinity to them. Please see the primary citation for more details. The Rvalues for the S and R isomers are the following: for S-isomer R=0.196, Rfree=0.296; for R-isomer R=0.204, Rfree=0.302. The other two compounds 9OH and 11O were modelled to the density, no refinement, no energy minimization. The structure is metastable and it is highly possible for substrates and products to be there simultaneously.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 4147 10 %RANDOM
Rwork0.196 ---
all0.2614 48693 --
obs0.196 41035 84 %-
Displacement parametersBiso mean: 35.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 0 89 529 7314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.130.375844540.32231904360738
2.13-2.290.33555840.2921524156
2.29-2.520.31627240.2572613166
2.52-2.880.32957600.2345696273
2.88-3.630.28188190.1816766080
3.63-400.26968150.143728777
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARH5.FETOPH5.FE
X-RAY DIFFRACTION313HPODS.PAR13HPODS.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shell
*PLUS
% reflection Rfree: 4 %

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