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- PDB-1hu9: LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL -

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Basic information

Entry
Database: PDB / ID: 1hu9
TitleLIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL
ComponentsLIPOXYGENASE-3
KeywordsOXIDOREDUCTASE / METALLOPROTEIN / FE(III) COMPLEX / PURPLE LIPOXYGENASE / ENZYME INHIBITOR
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
4-HYDROPEROXY-2-METHOXY-PHENOL / : / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, K. / Skrzypczak-Jankun, E. / McCabe, N.P. / Selman, S.H. / Jankun, J.
Citation
Journal: INT.J.MOL.MED. / Year: 2003
Title: Structure of curcumin in complex with lipoxygenase and its significance in cancer.
Authors: Skrzypczak-Jankun, E. / Zhou, K. / McCabe, N.P. / Selman, S.H. / Jankun, J.
#1: Journal: Int.J.Mol.Med. / Year: 2000
Title: Curcumin Inhibits Lipooxygenase by Binding to its Center Cavity: Theoretical and X-Ray Evidence
Authors: Skrzypczak-Jankun, E. / McCabe, N.P. / Selman, S.H. / Jankun, J.
#2: 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.
#3: 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.
#4: Journal: Biochemistry / Year: 1994
Title: Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase 3
Authors: Kramer, J.A. / Johnson, K.R. / Dunham, W.R. / Sands, R.H. / Funk Jr., M.O.
History
DepositionJan 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: refine_ls_shell / Item: _refine_ls_shell.percent_reflns_obs
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 9, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)97,1313
Polymers96,9191
Non-polymers2122
Water7,584421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.790, 137.320, 61.870
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LIPOXYGENASE-3 / EC 1.13.11.12 OXIDOREDUCTASE / L-3


Mass: 96919.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMPLEX WITH 4-HYDROPEROXY-2-METHOXY-PHENOL A PHOTODEGREDATION PRODUCT OF CURCUMIN
Source: (natural) Glycine max (soybean) / Strain: BEESON-80 CULTIVAR / References: UniProt: P09186, 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-4HM / 4-HYDROPEROXY-2-METHOXY-PHENOL


Mass: 156.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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, phosphate-citrate buffer, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 45106 / Num. obs: 45106 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1 / Num. unique all: 4304 / % possible all: 90.9

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Processing

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

1lnh


Resolution: 2.2→40 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: DISORDERED REGIONS 1-8 WERE OMITTED FROM CALCULATIONS. DISORDERED REGIONS 33-45 WERE INCLUDED IN THE REFINEMENT, HOWEVER, THE HIGH B-FACTOR INDICATE DISORDER AND LOW RELIABILITY FOR THIS ...Details: DISORDERED REGIONS 1-8 WERE OMITTED FROM CALCULATIONS. DISORDERED REGIONS 33-45 WERE INCLUDED IN THE REFINEMENT, HOWEVER, THE HIGH B-FACTOR INDICATE DISORDER AND LOW RELIABILITY FOR THIS LOOP. THE IRON BINDING SITE CONSISTS OF HIS 518, HIS 523, HIS 709 ASN 713, ILE 857 (C-TERMINAL) AND 4HM 861.THESE LIGANDS ARE ALL COVALENTLY BOUND TO IRON FE 858 IN AN OCTAHEDRAL COORDINATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3932 9.9 %RANDOM
Rwork0.185 ---
all0.2012 43180 --
obs0.185 39461 83.2 %-
Displacement parametersBiso mean: 35.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 12 421 7211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_improper_angle_d1.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.340.31185250.2621445256.6
2.34-2.520.29375630.2395519666.06
2.52-2.770.28816540.2278578073.01
2.77-3.170.27697050.20886374
3.17-40.26537520.164683886.37
4-400.25147336.60.14862051688986.11
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARFRG_NEW.FETOPFRG_NEW.FE
X-RAY DIFFRACTION3PAR.HMPTOP.HMP

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