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- PDB-7ttk: Stable-5-LOX -

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Basic information

Entry
Database: PDB / ID: 7ttk
TitleStable-5-LOX
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 / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / 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 / lipid oxidation / 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 / 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 / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / 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: 1.98 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: To Be Published
Title: Stable-5-LOX "closed"
Authors: Gilbert, N.C.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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)158,9844
Polymers158,8722
Non-polymers1122
Water13,547752
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)55.440, 203.197, 76.566
Angle α, β, γ (deg.)90.000, 110.240, 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.: 2
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: isolated from a natural source / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
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: Mar 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→101.6 Å / Num. obs: 107838 / % possible obs: 98.43 % / Redundancy: 2 % / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 9.55
Reflection shellResolution: 1.98→2.05 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 10149 / CC1/2: 0.425 / % possible all: 92.61

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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: 1.98→101.6 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 5264 4.88 %
Rwork0.1648 102552 -
obs0.1666 107816 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.49 Å2 / Biso mean: 47.3076 Å2 / Biso min: 22.93 Å2
Refinement stepCycle: final / Resolution: 1.98→101.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10918 0 2 752 11672
Biso mean--39.26 43.52 -
Num. residues----1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111212
X-RAY DIFFRACTIONf_angle_d1.08415222
X-RAY DIFFRACTIONf_dihedral_angle_d19.8594144
X-RAY DIFFRACTIONf_chiral_restr0.0581643
X-RAY DIFFRACTIONf_plane_restr0.0141975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.98-2.010.40261460.34562773291980
2.01-2.030.33561880.31543404359299
2.03-2.050.33041890.2963449363898
2.05-2.080.31541650.26953373353899
2.08-2.110.31961690.27093469363899
2.11-2.140.33571720.263134833655100
2.14-2.170.26031750.23813408358399
2.17-2.20.25831730.21293442361599
2.2-2.230.23371680.23447361599
2.23-2.270.21771760.18463474365099
2.27-2.310.23091740.18113478365299
2.31-2.350.20191690.18383385355499
2.35-2.40.24321690.17373455362499
2.4-2.440.23282020.1753407360999
2.44-2.50.1871760.1713423359998
2.5-2.560.22191900.17223403359399
2.56-2.620.20961680.180834943662100
2.62-2.690.24891770.179234443621100
2.69-2.770.23081850.17693493367899
2.77-2.860.22731420.17383450359299
2.86-2.960.2151880.17393420360899
2.96-3.080.22591660.1763469363599
3.08-3.220.21481680.16633411357998
3.22-3.390.20221820.15823430361299
3.39-3.60.20961790.13834563635100
3.6-3.880.17011980.128634523650100
3.88-4.270.13121980.11623441363999
4.27-4.890.1471670.11373362352997
4.89-6.160.14941810.141234933674100
6.16-101.60.18151640.16613464362898
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)
11.8475-0.0562-0.60043.83441.29382.9868-0.29260.3331-0.2701-0.6090.1972-0.0250.32030.03070.05940.5307-0.07680.02310.2467-0.01160.26617.77517.3093-30.3645
20.2684-0.1025-0.40690.6220.2461.14310.02040.0131-0.01530.0391-0.01790.1224-0.0164-0.0780.00510.281-0.00610.00550.24330.00840.28993.238927.0816.7284
30.9143-0.0967-0.71650.62190.11681.1843-0.0476-0.0085-0.02850.01090.01250.05660.04750.02060.03770.32020.0031-0.00630.26010.00090.285611.252323.74213.1566
42.1895-1.0597-0.25713.0969-0.28252.2097-0.0804-0.1896-0.00610.26540.18880.28-0.2708-0.1152-0.10740.42520.04620.12440.23180.03150.2805-13.442879.276635.401
50.55460.0947-0.20210.02740.21654.465-0.0587-0.04620.03240.12230.12220.1193-0.2674-0.5088-0.10170.3309-0.00440.01760.32380.0090.3782-14.104665.395610.3574
62.1217-0.1702-0.40991.15520.06831.35490.05180.07390.0005-0.1423-0.02010.0750.0168-0.0594-0.01810.37770.03710.03580.2540.02990.24016.574262.2027-15.252
70.2464-0.0373-0.28590.23290.07051.59180.03590.01890.01640.0117-0.0110.0463-0.060.0066-0.02060.34290.01450.04570.23640.01350.29873.419568.59097.7256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -12 through 112 )A-12 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 402 )A113 - 402
3X-RAY DIFFRACTION3chain 'A' and (resid 403 through 673 )A403 - 673
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 141 )B5 - 141
5X-RAY DIFFRACTION5chain 'B' and (resid 142 through 187 )B142 - 187
6X-RAY DIFFRACTION6chain 'B' and (resid 188 through 364 )B188 - 364
7X-RAY DIFFRACTION7chain 'B' and (resid 365 through 673 )B365 - 673

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