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- PDB-7ttl: Stable-5-LOX elongated Ha2 (4 copies ASU) -

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Basic information

Entry
Database: PDB / ID: 7ttl
TitleStable-5-LOX elongated Ha2 (4 copies ASU)
ComponentsArachidonate 5-lipoxygenase
KeywordsOXIDOREDUCTASE / Lipoxygenase / dioxygenase / membrane-binding
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, 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 5-lipoxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsGilbert, N.C. / Newcomer, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM143724-01 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Helical remodeling augments 5-lipoxygenase activity in the synthesis of proinflammatory mediators.
Authors: Gallegos, E.M. / Reed, T.D. / Mathes, F.A. / Guevara, N.V. / Neau, D.B. / Huang, W. / Newcomer, M.E. / Gilbert, N.C.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)317,9688
Polymers317,7454
Non-polymers2234
Water8,575476
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
2
D: 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
3
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
4
C: 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
Unit cell
Length a, b, c (Å)76.791, 204.547, 106.768
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 79436.242 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.43→102.27 Å / Num. obs: 217327 / % possible obs: 97.91 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 8.58
Reflection shellResolution: 2.43→2.517 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 11353 / CC1/2: 0.629

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O8Y

3o8y


Resolution: 2.43→102.27 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 3748 1.72 %
Rwork0.2147 213579 -
obs0.2158 217327 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.66 Å2 / Biso mean: 65.339 Å2 / Biso min: 24.82 Å2
Refinement stepCycle: final / Resolution: 2.43→102.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21195 0 4 476 21675
Biso mean--43.69 47.86 -
Num. residues----2607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.460.39831300.35637298742887
2.46-2.490.36581360.35227927806393
2.49-2.520.34831370.34937768790593
2.52-2.560.42211380.33797581771989
2.56-2.60.39961360.3477839797593
2.6-2.640.35621470.32188050819795
2.64-2.680.35441390.31978024816395
2.68-2.730.35971500.30728132828296
2.73-2.780.37021310.29887999813095
2.78-2.830.3991320.29188046817895
2.83-2.890.2871410.28128058819995
2.89-2.950.35621510.27558005815694
2.95-3.020.30991250.28877940806595
3.02-3.10.33451290.27257801793092
3.1-3.180.34521400.27787533767389
3.18-3.270.31051410.23718030817196
3.27-3.380.25481440.20748204834896
3.38-3.50.32171440.20238097824195
3.5-3.640.28031370.17878067820496
3.64-3.810.26431340.17468024815895
3.81-4.010.21551350.16897869800494
4.01-4.260.25461480.14897599774790
4.26-4.590.17871440.13988081822596
4.59-5.050.19431460.14278011815795
5.05-5.780.22081300.17238035816595
5.78-7.280.24841410.19967810795193
7.28-102.270.22411420.18357751789392
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)
13.2590.0651.25860.4138-0.11911.16370.12-0.0963-0.0986-0.0652-0.0414-0.02470.07190.005-0.0880.26650.01630.04590.2658-0.02160.466760.195620.7666156.7285
22.6484-0.9653-0.44092.58220.42451.5220.02640.3641-0.7788-0.26650.1934-0.82950.16340.3085-0.15420.3452-0.02190.09160.4596-0.16520.844576.61369.4458106.5796
37.7276-0.53222.03140.0725-0.23481.72650.10851.1097-0.9425-0.05950.1914-0.16010.12290.234-0.25250.4033-0.04110.09090.57060.05130.386753.092122.296695.106
42.9558-0.14230.17860.671-0.09120.39170.01830.290.0987-0.1370.00320.12920.0313-0.0722-0.01660.2585-0.01960.01720.25790.01470.296835.150426.9821109.0387
52.9016-0.41461.3820.9013-0.7031.25810.08150.3215-0.3993-0.1414-0.00710.07090.10730.0184-0.10030.29650.0130.06130.2984-0.1160.350639.024415.9579108.241
62.2012-0.62920.58161.8447-0.66381.08020.02770.19190.3879-0.15690.28830.5989-0.0606-0.3227-0.24060.398-0.0192-0.01780.48210.21991.25134.108477.6216103.265
71.5388-0.42070.1690.7253-0.01710.53940.03490.16750.6779-0.1148-0.1788-0.3392-0.08920.21870.14180.3652-0.04150.03840.40650.18370.813750.192259.8104105.7645
82.1312-1.74710.46074.4151.12462.65010.09360.40580.3587-0.58870.0153-0.4999-0.1390.5406-0.16450.352-0.0722-0.00990.49670.21990.910431.268861.8131100.6948
91.804-0.430.17740.60920.03020.3968-0.01410.10430.8378-0.0849-0.0163-0.0639-0.1310.06140.02640.384-0.0349-0.04610.3660.13551.012637.758968.6498111.0844
102.0575-0.198-0.3231.39770.16390.90220.03120.28250.3186-0.53750.23351.1061-0.2567-0.2751-0.20410.4897-0.0099-0.07050.49240.23641.737324.973387.1669154.1644
112.18540.02880.02491.8978-0.33050.42750.05710.24730.2622-0.3443-0.0509-0.13360.03730.1176-0.02570.4162-0.03830.04240.43390.02660.935862.297769.9539154.9058
122.49310.03-0.30191.9604-0.32750.70150.04030.13820.3545-0.2066-0.0516-0.1970.00520.01530.00570.33230.005-0.00630.33870.05710.858561.211269.3196159.5408
134.264-0.4405-0.07062.08040.26421.32450.07090.1814-0.5895-0.19210.0939-0.54420.1580.1923-0.13220.3109-0.01840.05310.3903-0.09520.779295.895717.3277153.9037
146.78133.92773.94583.39662.3182.2357-0.07550.7733-0.2381-0.26390.204-0.73880.08080.4516-0.19350.39440.00290.07760.4412-0.00750.270566.73520.5302140.3895
150.6151-0.6462-0.7532.33342.08994.1008-0.0873-0.1728-0.04460.1008-0.02610.15560.11660.02060.16350.202-0.0198-0.01050.3770.00760.600841.222529.1928158.6549
163.9713-0.48240.18921.07980.10040.32360.0282-0.05410.3186-0.0449-0.0278-0.0002-0.03680.02710.02170.259-0.01070.03460.2535-0.04070.43862.548932.5908161.5736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 532 through 673 )B532 - 673
2X-RAY DIFFRACTION2chain 'A' and (resid -12 through 141 )A-12 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 187 )A142 - 187
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 531 )A188 - 531
5X-RAY DIFFRACTION5chain 'A' and (resid 532 through 673 )A532 - 673
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 141 )C5 - 141
7X-RAY DIFFRACTION7chain 'C' and (resid 142 through 385 )C142 - 385
8X-RAY DIFFRACTION8chain 'C' and (resid 386 through 442 )C386 - 442
9X-RAY DIFFRACTION9chain 'C' and (resid 443 through 673 )C443 - 673
10X-RAY DIFFRACTION10chain 'D' and (resid -12 through 112 )D-12 - 112
11X-RAY DIFFRACTION11chain 'D' and (resid 113 through 285 )D113 - 285
12X-RAY DIFFRACTION12chain 'D' and (resid 286 through 673 )D286 - 673
13X-RAY DIFFRACTION13chain 'B' and (resid 5 through 151 )B5 - 151
14X-RAY DIFFRACTION14chain 'B' and (resid 152 through 196 )B152 - 196
15X-RAY DIFFRACTION15chain 'B' and (resid 197 through 289 )B197 - 289
16X-RAY DIFFRACTION16chain 'B' and (resid 290 through 531 )B290 - 531

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