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- PDB-3v98: S663D Stable-5-LOX -

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Basic information

Entry
Database: PDB / ID: 3v98
TitleS663D Stable-5-LOX
ComponentsArachidonate 5-lipoxygenase
KeywordsOXIDOREDUCTASE / Lipoxygenase / dioxygenase
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 / negative regulation of sprouting angiogenesis / Biosynthesis of Lipoxins (LX) / negative regulation of response to endoplasmic reticulum stress / Synthesis of 5-eicosatetraenoic acids / positive regulation of leukocyte adhesion to arterial endothelial cell / lipoxygenase pathway / Interleukin-18 signaling / dendritic cell migration / arachidonate metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / negative regulation of vascular wound healing / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Biosynthesis of maresins / regulation of cellular response to oxidative stress / leukotriene metabolic process / negative regulation of wound healing / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukocyte migration involved in inflammatory response / lipid oxidation / leukotriene biosynthetic process / long-chain fatty acid biosynthetic process / regulation of reactive oxygen species biosynthetic process / regulation of fat cell differentiation / nuclear envelope lumen / regulation of cytokine production involved in inflammatory response / negative regulation of endothelial cell proliferation / humoral immune response / positive regulation of bone mineralization / regulation of insulin secretion / negative regulation of angiogenesis / negative regulation of inflammatory response / nuclear matrix / nuclear envelope / glucose homeostasis / 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-1 / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site ...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-1 / 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. / 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: 2.07 Å
AuthorsGilbert, N.C. / Rui, Z. / Neau, D.B. / Waight, M. / Bartlett, S.G. / Boeglin, W.E. / Brash, A.R. / Newcomer, M.E.
CitationJournal: Faseb J. / Year: 2012
Title: Conversion of human 5-lipoxygenase to a 15-lipoxygenase by a point mutation to mimic phosphorylation at Serine-663.
Authors: Gilbert, N.C. / Rui, Z. / Neau, D.B. / Waight, M.T. / Bartlett, S.G. / Boeglin, W.E. / Brash, A.R. / Newcomer, M.E.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Feb 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_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_asym_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_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 5-lipoxygenase
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,0404
Polymers158,9292
Non-polymers1122
Water17,222956
1
A: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5202
Polymers79,4641
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)79,5202
Polymers79,4641
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.410, 202.503, 76.971
Angle α, β, γ (deg.)90.00, 109.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 79464.250 Da / Num. of mol.: 2
Mutation: F15H, W76G, L77S, C241A, C562A, K654E, K655N, K656L, S664A
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


Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP ENTRY P09917 RESIDUES 41-45 (PRO PHE TYR ASN ASP) WERE DELETED AND REPLACED WITH RESIDUES GS(GLY SER)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.88 %
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-C / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2010
RadiationMonochromator: Fast monochromatic rotary beam shutters with opening and closing times less than 5 msec, synchronized, precisely with the motion state of the crystallographic spindle.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.07→49.38 Å / Num. obs: 96485 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID
2.07-2.191
2.2-2.371
2.38-2.591
2.6-2.91
2.91-3.351
3.36-49.381

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→41.491 Å / SU ML: 0.48 / σ(F): 0.01 / Phase error: 18.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 1983 2.18 %2%
Rwork0.1664 ---
obs0.167 91112 94.27 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.132 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.2574 Å2-0 Å24.7395 Å2
2--0.5242 Å20 Å2
3----4.7816 Å2
Refinement stepCycle: LAST / Resolution: 2.07→41.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10920 0 2 956 11878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211238
X-RAY DIFFRACTIONf_angle_d0.69115249
X-RAY DIFFRACTIONf_dihedral_angle_d12.6744151
X-RAY DIFFRACTIONf_chiral_restr0.0431644
X-RAY DIFFRACTIONf_plane_restr0.0021978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.12180.25631210.22665579X-RAY DIFFRACTION83
2.1218-2.17910.25651280.21045871X-RAY DIFFRACTION87
2.1791-2.24330.21961420.1926044X-RAY DIFFRACTION90
2.2433-2.31570.23431290.18176173X-RAY DIFFRACTION91
2.3157-2.39840.23521480.17816226X-RAY DIFFRACTION93
2.3984-2.49440.22791330.17866291X-RAY DIFFRACTION93
2.4944-2.60790.24181460.18016378X-RAY DIFFRACTION95
2.6079-2.74540.21231450.17776453X-RAY DIFFRACTION96
2.7454-2.91740.18351460.17446566X-RAY DIFFRACTION97
2.9174-3.14260.22961470.1736563X-RAY DIFFRACTION98
3.1426-3.45870.18911530.1586716X-RAY DIFFRACTION99
3.4587-3.95880.16281490.13646729X-RAY DIFFRACTION99
3.9588-4.98630.13941500.12546742X-RAY DIFFRACTION100
4.9863-41.49940.18691460.1786798X-RAY DIFFRACTION100

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