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- PDB-4nre: The structure of human 15-lipoxygenase-2 with a substrate mimic -

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Basic information

Entry
Database: PDB / ID: 4nre
TitleThe structure of human 15-lipoxygenase-2 with a substrate mimic
ComponentsArachidonate 15-lipoxygenase B
KeywordsOXIDOREDUCTASE / Calcium Binding
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 / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen ...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 / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / regulation of epithelial cell differentiation / lipoxygenase pathway / positive regulation of peroxisome proliferator activated receptor signaling pathway / arachidonic acid metabolic process / lipid oxidation / prostate gland development / negative regulation of growth / positive regulation of macrophage derived foam cell differentiation / hepoxilin biosynthetic process / linoleic acid metabolic process / positive regulation of keratinocyte differentiation / negative regulation of cell cycle / phospholipid metabolic process / positive regulation of chemokine production / negative regulation of cell migration / adherens junction / lipid metabolic process / cytoskeleton / iron ion binding / negative regulation of cell population proliferation / focal adhesion / lipid binding / apoptotic process / calcium ion binding / extracellular exosome / membrane / nucleus / 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
: / Polyunsaturated fatty acid lipoxygenase ALOX15B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsKobe, M.J. / Neau, D.B. / Mitchell, C.E. / Bartlett, S.G. / Newcomer, M.E.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The structure of human 15-lipoxygenase-2 with a substrate mimic.
Authors: Kobe, M.J. / Neau, D.B. / Mitchell, C.E. / Bartlett, S.G. / Newcomer, M.E.
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Other
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_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: Arachidonate 15-lipoxygenase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,28321
Polymers78,1051
Non-polymers2,17820
Water6,630368
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Arachidonate 15-lipoxygenase B
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)481,697126
Polymers468,6296
Non-polymers13,067120
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area36970 Å2
ΔGint-1143 kcal/mol
Surface area151410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.794, 155.794, 263.219
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-707-

SO4

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 78104.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX15B / Plasmid: pETDuet-1 / 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, 388 molecules

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


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


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1M (NH4)2SO4, 0.1M BisTris pH 5.5, 5% Glycerol, 24mM C8E4, 40mM CaCl2 soak for 30 min, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2011
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.63→47.55 Å / Num. all: 34699 / Num. obs: 34599 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.63→2.77 Å / % possible all: 69.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→38.949 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2033 1999 5.79 %
Rwork0.1627 --
obs0.165 34553 94.06 %
all-34699 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→38.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5349 0 123 368 5840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065666
X-RAY DIFFRACTIONf_angle_d0.7217725
X-RAY DIFFRACTIONf_dihedral_angle_d13.5892085
X-RAY DIFFRACTIONf_chiral_restr0.028824
X-RAY DIFFRACTIONf_plane_restr0.003991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6302-2.6960.2944970.26311571X-RAY DIFFRACTION64
2.696-2.76880.3241110.26321808X-RAY DIFFRACTION74
2.7688-2.85030.29641260.27312071X-RAY DIFFRACTION84
2.8503-2.94220.33451480.24772404X-RAY DIFFRACTION98
2.9422-3.04740.26271500.23322436X-RAY DIFFRACTION100
3.0474-3.16930.25791500.21972447X-RAY DIFFRACTION100
3.1693-3.31350.26431490.20552433X-RAY DIFFRACTION100
3.3135-3.48810.24861520.192459X-RAY DIFFRACTION100
3.4881-3.70650.18951500.15582461X-RAY DIFFRACTION100
3.7065-3.99240.19181510.13872447X-RAY DIFFRACTION100
3.9924-4.39370.17311520.12622475X-RAY DIFFRACTION100
4.3937-5.02830.1591540.11382498X-RAY DIFFRACTION100
5.0283-6.33070.18881530.14092490X-RAY DIFFRACTION99
6.3307-38.95280.1421560.13482554X-RAY DIFFRACTION98
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)
11.64580.54920.10980.91360.32511.2855-0.20180.14230.1213-0.32620.05070.1095-0.04620.03060.14320.4782-0.0185-0.05720.31310.03530.303316.4804-45.8267-18.4069
23.08730.478-0.70911.21130.11681.4325-0.11670.04360.1343-0.1196-0.00720.28110.1081-0.18890.13340.4265-0.0724-0.06130.3304-0.0180.33913.2732-48.8239-12.9613
34.7656-0.1866-1.47743.6312-0.0994.2457-0.09060.4790.7036-0.1762-0.07440.6271-0.4234-0.6040.13640.46720.0284-0.19780.51360.03530.4855-6.2529-38.0034-23.6429
43.6832.75120.31854.09250.63582.9325-0.29540.517-0.1132-0.0453-0.10810.21930.7255-1.46180.44730.71-0.32450.03151.1141-0.11260.7433-31.0671-67.8862-21.2958
57.1857-5.7875-3.46815.1284.45797.671-0.01520.61440.1984-1.07370.1487-0.69840.44650.1044-0.12551.3613-0.23240.09821.053-0.01890.9036-22.8426-86.0081-27.6371
66.98483.09760.00372.88930.33183.4972-0.27070.31550.27680.0588-0.06790.56870.2891-0.99320.35750.4952-0.1734-0.04680.769-0.07630.6847-25.9774-61.1459-14.9615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 133 through 370 )
2X-RAY DIFFRACTION2chain 'A' and (resid 371 through 630 )
3X-RAY DIFFRACTION3chain 'A' and (resid 631 through 676 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 84 )
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 132 )

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