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- PDB-2p0m: Revised structure of rabbit reticulocyte 15S-lipoxygenase -

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Basic information

Entry
Database: PDB / ID: 2p0m
TitleRevised structure of rabbit reticulocyte 15S-lipoxygenase
ComponentsArachidonate 15-lipoxygenaseALOX15
KeywordsOXIDOREDUCTASE / rabbit / 15s-lipoxygenase / twin / pseudo symmetry / conformational change / arachidonate / iron
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 15-lipoxygenase / arachidonate 15-lipoxygenase activity / arachidonate 12(S)-lipoxygenase activity / linoleate 13S-lipoxygenase ...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 15-lipoxygenase / arachidonate 15-lipoxygenase activity / arachidonate 12(S)-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / phosphatidylethanolamine biosynthetic process / lipoxygenase pathway / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / arachidonic acid metabolic process / hepoxilin biosynthetic process / linoleic acid metabolic process / apoptotic cell clearance / positive regulation of cell-substrate adhesion / positive regulation of actin filament polymerization / bone mineralization / fatty acid oxidation / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / response to endoplasmic reticulum stress / lipid droplet / ossification / wound healing / lipid metabolic process / 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, iron binding site / Lipoxygenases iron-binding region signature 1. ...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, 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, / 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 / Resolution: 2.4 Å
AuthorsChoi, J. / Chon, J.K. / Kim, S. / Shin, W.
CitationJournal: 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.
History
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Sep 28, 2011Group: Other
Revision 1.3Mar 13, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0This entry 2P0M reflects an alternative modeling of the structural data in r1loxsf, original data ...This entry 2P0M reflects an alternative modeling of the structural data in r1loxsf, original data determined by author: S.A.GILLMOR,A.VILLASENOR,R.J.FLETTERICK,E.SIGAL,M.F.BROWNER

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arachidonate 15-lipoxygenase
B: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8915
Polymers150,5232
Non-polymers3683
Water3,927218
1
A: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3172
Polymers75,2621
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5743
Polymers75,2621
Non-polymers3122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-56 kcal/mol
Surface area53240 Å2
MethodPISA
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 number146
Space group name H-MH3

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Components

#1: Protein Arachidonate 15-lipoxygenase / ALOX15 / 15S-lipoxygenase / Omega-6 lipoxygenase / Erythroid cell-specific 15-lipoxygenase / 15-LOX


Mass: 75261.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P12530, arachidonate 15-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.25 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1LOX.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementResolution: 2.4→15.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 350253.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: The author created the R3 data from the original R32 data by equating |Fo(kh-l)| to |Fo(hkl)| using the computer program SFTOOLS in the CCP4 package with an option to generate the symmetry related reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 7394 9.7 %RANDOM
Rwork0.193 ---
obs0.193 76159 97.9 %-
all-78259 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9743 Å2 / ksol: 0.353654 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.4→15.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10592 0 21 218 10831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 1134 9.6 %
Rwork0.268 10739 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2HOHer.paramHOHer.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4rs7b.paramrs7b.top

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