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- PDB-8viy: 15-Lipoxygenase-2 V427L -

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Basic information

Entry
Database: PDB / ID: 8viy
Title15-Lipoxygenase-2 V427L
ComponentsPolyunsaturated fatty acid lipoxygenase ALOX15B
KeywordsOXIDOREDUCTASE / Lipoxygenase
Function / homology
Function and homology information


endocannabinoid signaling pathway / arachidonate 8(S)-lipoxygenase activity / lipoxin A4 biosynthetic process / cannabinoid biosynthetic process / linoleate 9S-lipoxygenase activity / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Synthesis of 15-eicosatetraenoic acid derivatives / linoleate 13S-lipoxygenase activity / lipoxygenase pathway ...endocannabinoid signaling pathway / arachidonate 8(S)-lipoxygenase activity / lipoxin A4 biosynthetic process / cannabinoid biosynthetic process / linoleate 9S-lipoxygenase activity / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Synthesis of 15-eicosatetraenoic acid derivatives / linoleate 13S-lipoxygenase activity / lipoxygenase pathway / regulation of epithelial cell differentiation / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of growth / arachidonate metabolic process / prostate gland development / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / positive regulation of keratinocyte differentiation / positive regulation of macrophage derived foam cell differentiation / negative regulation of cell cycle / positive regulation of chemokine production / phospholipid metabolic process / negative regulation of cell migration / adherens junction / lipid metabolic process / cytoskeleton / iron ion binding / negative regulation of cell population proliferation / focal adhesion / apoptotic process / lipid binding / calcium ion binding / extracellular exosome / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase ...Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / 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. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile.
Similarity search - Domain/homology
: / Polyunsaturated fatty acid lipoxygenase ALOX15B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGilbert, N.C. / Offenbacher, A.R. / Ohler, A.R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM143724-01 United States
CitationJournal: Acs Catalysis / Year: 2024
Title: Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence from Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers.
Authors: Ohler, A. / Taylor, P.E. / Bledsoe, J.A. / Iavarone, A.T. / Gilbert, N.C. / Offenbacher, A.R.
History
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyunsaturated fatty acid lipoxygenase ALOX15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,94528
Polymers78,1191
Non-polymers2,82727
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.406, 155.406, 263.405
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-709-

GOL

21A-709-

GOL

31A-722-

SO4

41A-807-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyunsaturated fatty acid lipoxygenase ALOX15B / 15-lipoxygenase 2 / 15-LOX-2 / Arachidonate 15-lipoxygenase B / 15-LOX-B / Arachidonate 15- ...15-lipoxygenase 2 / 15-LOX-2 / Arachidonate 15-lipoxygenase B / 15-LOX-B / Arachidonate 15-lipoxygenase type II / Linoleate 13-lipoxygenase 15-LOb


Mass: 78118.914 Da / Num. of mol.: 1 / Mutation: V427L
Source method: isolated from a genetically manipulated source
Details: C8E / Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX15B / Production host: Escherichia coli (E. coli)
References: UniProt: O15296, arachidonate 15-lipoxygenase, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen

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Non-polymers , 6 types, 168 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5. 1.0 (NH4)2SO4 5% glycerol 24 mM C8E4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→65.2 Å / Num. obs: 51410 / % possible obs: 99.56 % / Redundancy: 20.3 % / Biso Wilson estimate: 54.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.9
Reflection shellResolution: 2.34→2.43 Å / Num. unique obs: 4909 / CC1/2: 0.602 / % possible all: 96.63

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Processing

Software
NameVersionClassification
PHENIXdev_3908refinement
PHENIXdev_3908refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→65.2 Å / SU ML: 0.3434 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 2513 4.91 %
Rwork0.1841 48698 -
obs0.186 51211 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.64 Å2
Refinement stepCycle: LAST / Resolution: 2.34→65.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5350 0 164 141 5655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345673
X-RAY DIFFRACTIONf_angle_d1.2957716
X-RAY DIFFRACTIONf_chiral_restr0.0545824
X-RAY DIFFRACTIONf_plane_restr0.0088991
X-RAY DIFFRACTIONf_dihedral_angle_d13.311780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.390.39551170.3392541X-RAY DIFFRACTION94.26
2.39-2.440.29831300.28342687X-RAY DIFFRACTION99.65
2.44-2.490.28351450.25522673X-RAY DIFFRACTION99.93
2.49-2.550.27341410.24212689X-RAY DIFFRACTION99.93
2.55-2.610.26631450.23432697X-RAY DIFFRACTION99.79
2.61-2.680.27931360.2272690X-RAY DIFFRACTION99.89
2.68-2.760.29971560.23222656X-RAY DIFFRACTION99.86
2.76-2.850.27991330.24732719X-RAY DIFFRACTION99.89
2.85-2.950.29091690.25662646X-RAY DIFFRACTION99.89
2.95-3.070.29961300.23742724X-RAY DIFFRACTION99.89
3.07-3.210.28571420.21252719X-RAY DIFFRACTION99.9
3.21-3.380.25721530.20742678X-RAY DIFFRACTION99.89
3.38-3.590.23641550.20262704X-RAY DIFFRACTION99.76
3.59-3.870.21951290.16862728X-RAY DIFFRACTION99.9
3.87-4.260.17441400.14052719X-RAY DIFFRACTION100
4.26-4.880.17431110.13422791X-RAY DIFFRACTION99.97
4.88-6.140.18111580.15312748X-RAY DIFFRACTION100
6.14-65.20.18531230.16442889X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.05013925325-2.58602040031-1.465601237115.06504678819-0.3730738926771.00986020393-0.463467071715-0.9015286233490.50084744770.2599061129190.01959073916840.166350805208-0.584115949034-0.916867908690.4433004155150.7283629319510.236641695896-0.04321907269910.870066182723-0.1706240115090.655954313802-31.683874114767.262068476522.4669215262
21.53479656493-1.85766427312-1.303892812972.899336841270.6481691127212.39734928945-0.138290323233-0.1394950210510.0546642919233-0.0763937241108-0.1404357389410.149241491869-0.474883545708-0.7071168185030.2591659858430.6722658431610.189360970289-0.08101021524540.807132234636-0.04524071901340.763737211928-25.654575828665.594038301617.1481191765
31.02741332036-0.1696817666680.1369786398110.5037314374940.1814306204551.02015846632-0.103722238668-0.124362773270.01561115867250.1473952232620.04511656599250.00586081469610.01945997696970.1179597350640.05184401670840.5964589311770.01400506419420.002707298269580.4882526506910.009881442347220.45737121740616.279503468945.593045736618.3701777226
42.08507457118-0.2204132592020.5039740669750.8698779848620.01584609095261.14917767081-0.077117023221-0.123162871938-0.007454869305280.09571488763470.00213520580110.145749511311-0.0505349017173-0.08250573059690.0668441885020.5892964982870.05659118761650.01680143871540.497082131826-0.003001664929540.4993255029931.8139945203746.926839739614.6697256538
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 63 )2 - 631 - 62
22chain 'A' and (resid 64 through 131 )64 - 13163 - 130
33chain 'A' and (resid 132 through 370 )132 - 370131 - 369
44chain 'A' and (resid 371 through 676 )371 - 676370 - 675

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