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- PDB-1lox: RABBIT RETICULOCYTE 15-LIPOXYGENASE -

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Basic information

Entry
Database: PDB / ID: 1lox
TitleRABBIT RETICULOCYTE 15-LIPOXYGENASE
Components15-LIPOXYGENASE
KeywordsOXIDOREDUCTASE / 15LO_DEPOT2
Function / homology
Function and homology information


cellular response to interleukin-13 / regulation of engulfment of apoptotic cell / negative regulation of adaptive immune response / regulation of peroxisome proliferator activated receptor signaling pathway / arachidonate 12-lipoxygenase / lipoxin A4 biosynthetic process / arachidonate 12(S)-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / phosphatidylethanolamine biosynthetic process ...cellular response to interleukin-13 / regulation of engulfment of apoptotic cell / negative regulation of adaptive immune response / regulation of peroxisome proliferator activated receptor signaling pathway / arachidonate 12-lipoxygenase / lipoxin A4 biosynthetic process / arachidonate 12(S)-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / phosphatidylethanolamine biosynthetic process / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / apoptotic cell clearance / positive regulation of cell-substrate adhesion / positive regulation of actin filament polymerization / bone mineralization / fatty acid oxidation / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / ossification / arachidonate metabolic process / hepoxilin biosynthetic process / linoleic acid metabolic process / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / response to endoplasmic reticulum stress / lipid droplet / lipid metabolic process / wound healing / cytoplasmic side of plasma membrane / regulation of inflammatory response / positive regulation of ERK1 and ERK2 cascade / iron ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / 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-1 / Lipoxygenase homology 2 (beta barrel) domain ...Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / 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-1 / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / (2E)-3-(2-OCT-1-YN-1-YLPHENYL)ACRYLIC ACID / Polyunsaturated fatty acid lipoxygenase ALOX15
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsGillmor, S.A. / Villasenor, A. / Fletterick, R.J. / Sigal, E. / Browner, M.F.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity.
Authors: Gillmor, S.A. / Villasenor, A. / Fletterick, R. / Sigal, E. / Browner, M.F.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Erratum. The Structure of Mammalian 15-Lipoxygenase Reveals Similarity to the Lipases and the Determinants of Substrate Specificity
Authors: Gillmor, S.A. / Villasenor, A. / Fletterick, R. / Sigal, E. / Browner, M.F.
History
DepositionOct 6, 1997Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 16, 2015Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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: 15-LIPOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5653
Polymers75,2531
Non-polymers3122
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.900, 198.900, 136.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein 15-LIPOXYGENASE / 15LOX


Mass: 75252.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 15LOX IS BOUND TO A COMPETITIVE INHIBITOR WHICH HAS THE RESIDUE NUMBER 841
Source: (natural) Oryctolagus cuniculus (rabbit) / Cell: RETICULOCYTE / Cellular location: CYTOPLASM / References: UniProt: P12530, arachidonate 15-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-RS7 / (2E)-3-(2-OCT-1-YN-1-YLPHENYL)ACRYLIC ACID


Mass: 256.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCARBOXY TERMINUS IS ONE OF THE LIGANDS TO THE CATALYTIC FE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 63 %
Crystal growpH: 7.5 / Details: PEG PH 7.5
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
190 mg/mlprotein1drop
30.48 M1dropLi2SO4
450-200 mMHEPES1drop
50.5-2 %mPEG50001drop
60.45 M1reservoirLi2SO4
7100 mMHEPES1reservoir
81 %mPEG50001reservoir
2inhibitor1drop2-fold molar excess

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 39151 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.33 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.362 / % possible all: 95.7
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→16 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: EARLY ROUNDS OF REFINEMENT WERE DONE WITH THE PROGRAM REFMAC FROM CCP4
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -5 %RANDOM
Rwork0.198 ---
obs0.198 39132 98 %-
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5109 0 20 94 5223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.33
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.4
X-RAY DIFFRACTIONx_mcangle_it3.7
X-RAY DIFFRACTIONx_scbond_it2.4
X-RAY DIFFRACTIONx_scangle_it3.7
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.341 -5 %
Rwork0.322 4501 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33
LS refinement shell
*PLUS
Rfactor obs: 0.322

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