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- PDB-1n8q: LIPOXYGENASE IN COMPLEX WITH PROTOCATECHUIC ACID -

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Basic information

Entry
Database: PDB / ID: 1n8q
TitleLIPOXYGENASE IN COMPLEX WITH PROTOCATECHUIC ACID
Componentslipoxygenase-3
KeywordsOXIDOREDUCTASE / lipoxygenase / iron / protocatechuic acid / 3 / 4-dihydroxybenzoic acid / lox complex / quercetin
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
3,4-DIHYDROXYBENZOIC ACID / : / Seed linoleate 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBorbulevych, O.Y. / Jankun, J. / Selman, S.H. / Skrzypczak-Jankun, E.
Citation
Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004
Title: Lipoxygenase interactions with natural flavonoid, quercetin, reveal a complex with protocatechuic acid in its X-ray structure at 2.1 A resolution.
Authors: Borbulevych, O.Y. / Jankun, J. / Selman, S.H. / Skrzypczak-Jankun, E.
#1: Journal: Biochemistry / Year: 1998
Title: Structural and thermochemical characterization of lipoxygenase-catechol complexes
Authors: Pham, C.H. / Jankun, J. / Skrzypczak-Jankun, E. / Flowers II, R.A. / Funk Jr., M.O.
#2: 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
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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 / 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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)97,1293
Polymers96,9191
Non-polymers2102
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.645, 136.961, 61.799
Angle α, β, γ (deg.)90.00, 95.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1441-

HOH

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Components

#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: Resnick 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-DHB / 3,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.34 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: PEG 8000, citrate-phosphate buffer, tris HCl, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7 / Method: vapor diffusion, sitting drop / Details: Skrzypczak-Jankun, E., (1997) Proteins, 29, 15.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.1 MTris-HCl1droppH7.
320 %(w/v)PEG80001reservoir
40.05 Mcitrate-phosphate1reservoirpH4.6
50.2 %(w/v)1reservoirNaN3
60.1 Msodium phosphate1reservoirpH7.

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2002 / Details: Focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 54294 / Num. obs: 52285 / % possible obs: 0.963 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.36 / Num. unique all: 4668 / % possible all: 86.2
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / Num. obs: 52281 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 86.2 % / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREPfrom CCP4phasing
REFMAC5.1.24refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IK3

1ik3


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.608 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic thermal model / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2659 5.1 %RANDOM
Rwork0.189 ---
all0.192 52281 --
obs0.192 49622 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.753 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20.73 Å2
2--0.29 Å20 Å2
3----1.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 12 463 7253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216967
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9569455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5795848
X-RAY DIFFRACTIONr_chiral_restr0.1360.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025335
X-RAY DIFFRACTIONr_nbd_refined0.1770.073132
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.4633
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.0755
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.414
X-RAY DIFFRACTIONr_mcbond_it1.58924238
X-RAY DIFFRACTIONr_mcangle_it2.63136870
X-RAY DIFFRACTIONr_scbond_it1.89322727
X-RAY DIFFRACTIONr_scangle_it2.66432585
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.393 189
Rwork0.297 3204
obs-3204
Refinement TLS params.Method: refined / Origin x: 27.3399 Å / Origin y: 0.503 Å / Origin z: 15.2134 Å
111213212223313233
T0.0072 Å20.0199 Å2-0.0186 Å2-0.0584 Å2-0.057 Å2--0.0574 Å2
L0.9669 °20.3285 °2-0.374 °2-1.4012 °2-0.3496 °2--1.4628 °2
S-0.0174 Å °0.0238 Å °-0.0146 Å °0.0257 Å °0.0625 Å °0.1222 Å °0.0114 Å °-0.1713 Å °-0.0451 Å °
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.05
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg7.58

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