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- PDB-1jnq: LIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH EPIGALLOCATHECHIN (EGC) -

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Basic information

Entry
Database: PDB / ID: 1jnq
TitleLIPOXYGENASE-3 (SOYBEAN) COMPLEX WITH EPIGALLOCATHECHIN (EGC)
Componentslipoxygenase-3
KeywordsOXIDOREDUCTASE / METALLOPROTEIN / FE(II) COMPLEX / PURPLE LIPOXYGENASE / CATECHIN INHIBITOR / GREEN TEA
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
2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL / : / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhou, K. / Skrzypczak-Jankun, E. / Jankun, J.
Citation
Journal: INT.J.MOL.MED. / Year: 2003
Title: Inhibition of lipoxygenase by (-)-epigallocatechin gallate: X-ray analysis at 2.1 A reveals degradation of EGCG and shows soybean LOX-3 complex with EGC instead.
Authors: Skrzypczak-Jankun, E. / Zhou, K. / Jankun, J.
#1: Journal: Nature / Year: 1997
Title: Why Drinking Green Tea Could Prevent Cancer
Authors: Jankun, J. / Selman, S.H. / Swiercz, R. / Skrzypczak-Jankun, E.
#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: Proteins: Struct.,Funct.,Genet. / 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.
#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
DepositionJul 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: KABSCH & SANDER (AUTHOR PROVIDED).
Remark 700SHEET DETERMINATION METHOD: KABSCH & SANDER (AUTHOR PROVIDED). STRAND: S1 1; N-TERMINAL 8-STRANDED ...SHEET DETERMINATION METHOD: KABSCH & SANDER (AUTHOR PROVIDED). STRAND: S1 1; N-TERMINAL 8-STRANDED BETA BARREL.
Remark 999SEQUENCE SEQUENCE AS DEPOSITED FOR LOX3_SOYBN IN SWISS-PROT P09186 WITH CHANGES AS FOR CV.PROVAR ...SEQUENCE SEQUENCE AS DEPOSITED FOR LOX3_SOYBN IN SWISS-PROT P09186 WITH CHANGES AS FOR CV.PROVAR (REFERENCE 4). SEQUENCES OF L3 IN STRAINS HAWKEYE AND PROVAR DIFFER OF 5 AMINO ACIDS OUT OF 857. ALL 5 MUTATIONS ARE NOT IN THE ACTIVE SITE REGION THAT IS HIGHLY CONSERVED. SEQUENCE OF THE STRAIN BEESON-80 CULTIVAR IS NOT DEPOSITED. NO EVIDENCE IN THE ELECTRON DENSITY MAP HAS BEEN NOTICED THAT WOULD JUSTIFY ANY SUGGESTIONS CONCERNING PRESENCE OF MUTATIONS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lipoxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2813
Polymers96,9191
Non-polymers3622
Water9,224512
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.730, 137.270, 61.88
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein lipoxygenase-3 / L-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
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EGT / 2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL / EPIGALLOCATECHIN


Mass: 306.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 3

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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

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 12, 1997 / Details: Focusing mirrors
RadiationMonochromator: Focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 50811 / Num. obs: 43096 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5095 / % possible all: 94.1

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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: 2.1→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 4338 10 %RANDOM
Rwork0.199 ---
all0.256 50811 --
obs0.232 43096 80.5 %-
Displacement parametersBiso mean: 31.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 23 512 7313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_improper_angle_d1.39
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
2.1-2.230.29535380.19894769
2.23-2.40.29336420.19355856
2.4-2.630.29086910.18576521
2.63-2.990.2857960.17536849
2.99-3.710.27618380.16197284
3.71-80.26118335.20.149826717479
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR28.FETOP.FE
X-RAY DIFFRACTION3PAR.EGCTOP.EGC

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