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- PDB-8x8f: Crystal structure of lipoxygenase from Enhygromyxa salina -

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Basic information

Entry
Database: PDB / ID: 8x8f
TitleCrystal structure of lipoxygenase from Enhygromyxa salina
ComponentsArachidonate 15-lipoxygenase
KeywordsOXIDOREDUCTASE / 9-lipoxygenase
Function / homology
Function and homology information


lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding
Similarity search - Function
Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile.
Similarity search - Domain/homology
: / Arachidonate 15-lipoxygenase
Similarity search - Component
Biological speciesEnhygromyxa salina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.796 Å
AuthorsKim, J.W. / Seo, P.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of lipoxygenase from Enhygromyxa salina
Authors: Kim, J.W. / Seo, P.W.
History
DepositionNov 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arachidonate 15-lipoxygenase
B: Arachidonate 15-lipoxygenase
C: Arachidonate 15-lipoxygenase
D: Arachidonate 15-lipoxygenase
E: Arachidonate 15-lipoxygenase
F: Arachidonate 15-lipoxygenase
G: Arachidonate 15-lipoxygenase
H: Arachidonate 15-lipoxygenase
I: Arachidonate 15-lipoxygenase
J: Arachidonate 15-lipoxygenase
K: Arachidonate 15-lipoxygenase
L: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)852,44760
Polymers847,05112
Non-polymers5,39648
Water17,114950
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Arachidonate 15-lipoxygenase
E: Arachidonate 15-lipoxygenase
F: Arachidonate 15-lipoxygenase
J: Arachidonate 15-lipoxygenase
K: Arachidonate 15-lipoxygenase
hetero molecules

A: Arachidonate 15-lipoxygenase
B: Arachidonate 15-lipoxygenase
L: Arachidonate 15-lipoxygenase
hetero molecules

C: Arachidonate 15-lipoxygenase
G: Arachidonate 15-lipoxygenase
I: Arachidonate 15-lipoxygenase
hetero molecules

H: Arachidonate 15-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)852,44760
Polymers847,05112
Non-polymers5,39648
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_757-x+2,y+1/2,-z+21
Buried area15480 Å2
ΔGint-175 kcal/mol
Surface area263000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.726, 248.590, 164.089
Angle α, β, γ (deg.)90.000, 119.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arachidonate 15-lipoxygenase / 9S-lipoxygenase


Mass: 70587.570 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enhygromyxa salina (bacteria) / Gene: DB30_08017 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0C2CV93
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.4M Magnesium chloride, 20mM Cadmium chloride, 0.1M Tris-HCl pH 8.5, 13.5% (w/v) PEG 2000, 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.796→50 Å / Num. obs: 258691 / % possible obs: 92.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.23 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.069 / Rrim(I) all: 0.157 / Χ2: 0.888 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.50.397109270.320.2670.4820.31778.1
2.85-2.92.80.422118370.20.2770.5090.37785
2.9-2.962.90.425120230.1840.2730.5080.486.1
2.96-3.023.10.394121850.4060.2420.4660.40387.4
3.02-3.083.30.378124310.4740.2260.4430.42389
3.08-3.153.30.358125130.5710.210.4180.42589.4
3.15-3.233.50.335127300.6590.1920.3890.45590.5
3.23-3.323.60.307127350.6860.1730.3550.46991.6
3.32-3.423.70.269128040.810.1510.3110.5191.2
3.42-3.533.90.23125390.9250.1230.2630.52289.8
3.53-3.654.40.213133320.9490.1080.240.6295.4
3.65-3.84.60.191133950.9620.0940.2140.67896.1
3.8-3.974.80.17135470.970.0820.1890.7796.5
3.97-4.1850.152136090.9770.0710.1690.88597.3
4.18-4.445.10.131136780.9860.0610.1461.06397.2
4.44-4.795.40.119132350.9890.0540.1311.19694.8
4.79-5.275.80.116138250.990.0510.1271.13998.7
5.27-6.035.70.12138750.9880.0530.1310.9998.8
6.03-7.595.80.102135520.9920.0440.1111.20696.2
7.59-506.60.076139190.9950.0310.0831.92897.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G32

4g32


Resolution: 2.796→49.611 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 9992 3.86 %
Rwork0.2268 248594 -
obs0.2279 258586 91.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.94 Å2 / Biso mean: 53.7926 Å2 / Biso min: 25.84 Å2
Refinement stepCycle: final / Resolution: 2.796→49.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55682 0 48 950 56680
Biso mean--80 35.71 -
Num. residues----7239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00357136
X-RAY DIFFRACTIONf_angle_d0.58778038
X-RAY DIFFRACTIONf_chiral_restr0.0428664
X-RAY DIFFRACTIONf_plane_restr0.00810281
X-RAY DIFFRACTIONf_dihedral_angle_d11.29334130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7964-2.82820.38712450.3603577764
2.8282-2.86140.36393070.363740783
2.8614-2.89630.36822810.3412769885
2.8963-2.9330.34763050.3333769486
2.933-2.97160.36483020.3392776586
2.9716-3.01230.35843220.3217792188
3.0123-3.05530.34223320.3142795388
3.0553-3.10090.33693290.3089807790
3.1009-3.14930.33673350.3104801490
3.1493-3.2010.32693220.2928811690
3.201-3.25620.30633200.2868819591
3.2562-3.31540.31053430.2761828692
3.3154-3.37910.30913230.2737825292
3.3791-3.44810.28623180.2623793588
3.4481-3.5230.2823370.2594818891
3.523-3.60490.27353630.2367856895
3.6049-3.69510.2593390.225861996
3.6951-3.79490.26453670.22866896
3.7949-3.90660.23353360.2058866696
3.9066-4.03260.22643340.2084881797
4.0326-4.17670.22113630.1948872197
4.1767-4.34380.19543640.1848884698
4.3438-4.54140.1983360.1762840094
4.5414-4.78060.18393450.1612873297
4.7806-5.07990.19423580.1688891199
5.0799-5.47160.20323660.1803892799
5.4716-6.02140.22343480.1933892599
6.0214-6.89070.2443500.1974861995
6.8907-8.67410.20763440.1744901099
8.6741-49.6110.22183580.2007888797
Refinement TLS params.Method: refined / Origin x: 76.0798 Å / Origin y: 58.6333 Å / Origin z: 88.1639 Å
111213212223313233
T0.316 Å20.0219 Å2-0.012 Å2-0.339 Å2-0.0366 Å2--0.3239 Å2
L0.0443 °20.0041 °20.0092 °2-0.0433 °2-0.0153 °2--0.0233 °2
S-0.0035 Å °0.0065 Å °0.0076 Å °0.0114 Å °0.0182 Å °-0.0123 Å °0.0084 Å °-0.0121 Å °-0.0138 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 650
2X-RAY DIFFRACTION1allA701 - 704
3X-RAY DIFFRACTION1allB3 - 650
4X-RAY DIFFRACTION1allB701 - 704
5X-RAY DIFFRACTION1allC3 - 650
6X-RAY DIFFRACTION1allC701 - 704
7X-RAY DIFFRACTION1allD3 - 650
8X-RAY DIFFRACTION1allD701 - 704
9X-RAY DIFFRACTION1allE3 - 650
10X-RAY DIFFRACTION1allE701 - 704
11X-RAY DIFFRACTION1allF3 - 650
12X-RAY DIFFRACTION1allF701 - 704
13X-RAY DIFFRACTION1allG3 - 650
14X-RAY DIFFRACTION1allG701 - 704
15X-RAY DIFFRACTION1allH3 - 650
16X-RAY DIFFRACTION1allH701 - 704
17X-RAY DIFFRACTION1allI3 - 650
18X-RAY DIFFRACTION1allI701 - 704
19X-RAY DIFFRACTION1allJ3 - 650
20X-RAY DIFFRACTION1allJ701 - 704
21X-RAY DIFFRACTION1allK3 - 650
22X-RAY DIFFRACTION1allK701 - 704
23X-RAY DIFFRACTION1allL3 - 650
24X-RAY DIFFRACTION1allL701 - 704
25X-RAY DIFFRACTION1allN1 - 994

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