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- PDB-3o8y: Stable-5-Lipoxygenase -

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Basic information

Entry
Database: PDB / ID: 3o8y
TitleStable-5-Lipoxygenase
ComponentsArachidonate 5-lipoxygenase
KeywordsOXIDOREDUCTASE / PLAT / LOX / Dioxygenase / Coactosin like protein / Five Lipoxygenase Activating Protein / Nuclear membrane / cytosol
Function / homology
Function and homology information


arachidonate 5-lipoxygenase / regulation of inflammatory response to wounding / leukotriene A4 biosynthetic process / lipoxin biosynthetic process / Biosynthesis of DPAn-3-derived protectins and resolvins / Biosynthesis of DPAn-3-derived 13-series resolvins / arachidonate 8(S)-lipoxygenase activity / leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives ...arachidonate 5-lipoxygenase / regulation of inflammatory response to wounding / leukotriene A4 biosynthetic process / lipoxin biosynthetic process / Biosynthesis of DPAn-3-derived protectins and resolvins / Biosynthesis of DPAn-3-derived 13-series resolvins / arachidonate 8(S)-lipoxygenase activity / leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Biosynthesis of DPAn-3-derived maresins / arachidonate 12(S)-lipoxygenase activity / leukocyte chemotaxis involved in inflammatory response / Synthesis of Lipoxins (LX) / negative regulation of response to endoplasmic reticulum stress / negative regulation of sprouting angiogenesis / Synthesis of 5-eicosatetraenoic acids / positive regulation of leukocyte adhesion to arterial endothelial cell / lipoxygenase pathway / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Interleukin-18 signaling / dendritic cell migration / arachidonic acid metabolic process / negative regulation of vascular wound healing / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / lipid oxidation / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of maresins / regulation of cellular response to oxidative stress / leukotriene metabolic process / negative regulation of wound healing / hepoxilin biosynthetic process / leukocyte migration involved in inflammatory response / Synthesis of Leukotrienes (LT) and Eoxins (EX) / linoleic acid metabolic process / leukotriene biosynthetic process / regulation of reactive oxygen species biosynthetic process / long-chain fatty acid biosynthetic process / regulation of fat cell differentiation / nuclear envelope lumen / negative regulation of endothelial cell proliferation / regulation of cytokine production involved in inflammatory response / regulation of insulin secretion / humoral immune response / positive regulation of bone mineralization / negative regulation of angiogenesis / negative regulation of inflammatory response / nuclear matrix / glucose homeostasis / nuclear envelope / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / iron ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / extracellular space / extracellular region / nucleoplasm / 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 5-lipoxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.389 Å
AuthorsNewcomer, M.E. / Gilbert, N.C. / Bartlett, S.G. / Waight, M.T. / Neau, D.B. / Boeglin, W.E. / Brash, A.R.
CitationJournal: Science / Year: 2011
Title: The structure of human 5-lipoxygenase.
Authors: Gilbert, N.C. / Bartlett, S.G. / Waight, M.T. / Neau, D.B. / Boeglin, W.E. / Brash, A.R. / Newcomer, M.E.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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_asym_id / _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_asym_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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arachidonate 5-lipoxygenase
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,9844
Polymers158,8722
Non-polymers1122
Water12,106672
1
A: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.170, 202.890, 76.800
Angle α, β, γ (deg.)90.00, 109.56, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 5:673 ) and (not element H) and (not element D)
211chain B and (resseq 5:673 ) and (not element H) and (not element D)

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Components

#1: Protein Arachidonate 5-lipoxygenase / / Stable-5-Lipoxygenase / 5-lipoxygenase / 5-LO


Mass: 79436.242 Da / Num. of mol.: 2
Mutation: delete 41-45 and replace with GS, W14E, F15H, W76G, L77S, C241A, C562A, KKK654-656ENL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX5, LOG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P09917, arachidonate 5-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETE RESIDUE 40-44 AND REPLACE WITH GS

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% tacsimate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2010
RadiationMonochromator: Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.389→40.77 Å / Num. obs: 62734 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.39→2.45 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.389→40.77 Å / SU ML: 0.27 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 1895 3.2 %3.2%
Rwork0.1824 ---
all0.1824 62734 --
obs0.1833 59131 94.23 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.947 Å2 / ksol: 0.405 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3069 Å2-0 Å26.4768 Å2
2---1.1465 Å20 Å2
3----2.1604 Å2
Refinement stepCycle: LAST / Resolution: 2.389→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10925 0 2 672 11599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311220
X-RAY DIFFRACTIONf_angle_d0.71415233
X-RAY DIFFRACTIONf_dihedral_angle_d13.6094148
X-RAY DIFFRACTIONf_chiral_restr0.0471644
X-RAY DIFFRACTIONf_plane_restr0.0031976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5434X-RAY DIFFRACTIONPOSITIONAL
12B5434X-RAY DIFFRACTIONPOSITIONAL0.017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3889-2.47420.2841730.24795238X-RAY DIFFRACTION87
2.4742-2.57330.26551730.23795330X-RAY DIFFRACTION88
2.5733-2.69040.24891770.23595465X-RAY DIFFRACTION90
2.6904-2.83220.28521950.21995541X-RAY DIFFRACTION92
2.8322-3.00960.24691860.2165738X-RAY DIFFRACTION94
3.0096-3.24190.24671960.20285845X-RAY DIFFRACTION97
3.2419-3.56790.2152000.17535923X-RAY DIFFRACTION98
3.5679-4.08380.15031920.14226006X-RAY DIFFRACTION99
4.0838-5.14360.15472030.13276067X-RAY DIFFRACTION99
5.1436-40.77580.18232000.16626083X-RAY DIFFRACTION99

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