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- PDB-9o4t: RT XFEL structure of Soybean Lipoxygenase-1 in large unit-cell -

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Basic information

Entry
Database: PDB / ID: 9o4t
TitleRT XFEL structure of Soybean Lipoxygenase-1 in large unit-cell
ComponentsSeed linoleate 13S-lipoxygenase-1
KeywordsOXIDOREDUCTASE / lipoxygenase / hydrated / solvent / dynamics
Function / homology
Function and homology information


linolenate 9R-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid oxidation / fatty acid biosynthetic process / iron ion binding / cytoplasm
Similarity search - Function
Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / 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, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / 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
: / Seed linoleate 13S-lipoxygenase-1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWolff, A.M. / Thompson, M.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-2231082 United States
Department of Energy (DOE, United States)DE-SC0024268 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: To Be Published
Title: Hydration of soybean lipoxygenase crystals is coupled to intramolecular dynamics
Authors: Wolff, A.M. / Paley, D.W. / Follmer, A.H. / Young, I.D. / Deary, A. / Hirschman, J. / Horani, A. / Lemons, R. / Lisova, S. / McAnelly, R.L. / Moreland, D. / Mous, S.T.M. / Ohler, A. / ...Authors: Wolff, A.M. / Paley, D.W. / Follmer, A.H. / Young, I.D. / Deary, A. / Hirschman, J. / Horani, A. / Lemons, R. / Lisova, S. / McAnelly, R.L. / Moreland, D. / Mous, S.T.M. / Ohler, A. / Rodriguez, J.M. / Russi, S. / Sierra, R.G. / Carbajo, S. / Poitevin, F.P. / Klinman, J.P. / Sauter, N.K. / Wilson, M.A. / Offenbacher, A.R. / Brewster, A.S. / Thompson, M.C.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Seed linoleate 13S-lipoxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5782
Polymers94,5221
Non-polymers561
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.031, 94.536, 50.529
Angle α, β, γ (deg.)90.000, 91.181, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Seed linoleate 13S-lipoxygenase-1 / Lipoxygenase-1 / L-1


Mass: 94522.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: LOX1.1, LOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08170, linoleate 13S-lipoxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 5.5
Details: In a 2 mL Eppendorf Tube, 0.5 mL of precipitant (0.4M NaOAc pH=5.5, 16% PEG-3350) and 0.5 mL of SLO (10 mg/mL in 50 mM NaOAc, pH=5.0) was combined together with ~10uL of seed stock (see 2.2. ...Details: In a 2 mL Eppendorf Tube, 0.5 mL of precipitant (0.4M NaOAc pH=5.5, 16% PEG-3350) and 0.5 mL of SLO (10 mg/mL in 50 mM NaOAc, pH=5.0) was combined together with ~10uL of seed stock (see 2.2.1.) being added to the tube cap prior to mixing by inversion. The tube was then placed on a Thermo Fisher Tuber Revolver Rotator, set to 30 RPM. Samples were left to mix overnight. Subsequently, samples were mixed in a ~1:1 ratio with 18% hydroxyethylcellulose (Sigma-Aldrich PN-09368) dissolved in SLO precipitant (0.4M NaOAc pH=5.5, 16% PEG-3350)

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.31 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Dec 12, 2022 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.31 Å / Relative weight: 1
ReflectionResolution: 1.95→19.59 Å / Num. obs: 65618 / % possible obs: 98.9 % / Redundancy: 77.59 % / Biso Wilson estimate: 37.02 Å2 / CC1/2: 0.989 / R split: 0.109 / Net I/σ(I): 4.416
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 12.19 % / Num. unique obs: 4590 / CC1/2: 0.567 / R split: 0.618 / % possible all: 99.78
Serial crystallography measurementFocal spot size: 75 µm2 / Pulse duration: 30 fsec. / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: 9% HEC injected via LCP style injector / Method: injection
Serial crystallography sample delivery injectionDescription: LCP-style injector
Serial crystallography data reductionLattices indexed: 34631

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.59 Å / SU ML: 0.2647 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.8012
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 2012 3.07 %
Rwork0.2124 63606 -
obs0.2131 65618 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 1 270 6529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286617
X-RAY DIFFRACTIONf_angle_d0.54239060
X-RAY DIFFRACTIONf_chiral_restr0.04081000
X-RAY DIFFRACTIONf_plane_restr0.00561187
X-RAY DIFFRACTIONf_dihedral_angle_d11.96212407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.36391370.31284453X-RAY DIFFRACTION99.05
2-2.050.31091400.29334506X-RAY DIFFRACTION100
2.05-2.110.30951430.28064553X-RAY DIFFRACTION100
2.11-2.180.27381440.26234546X-RAY DIFFRACTION100
2.18-2.260.30131510.26744491X-RAY DIFFRACTION100
2.26-2.350.28251380.25434555X-RAY DIFFRACTION100
2.35-2.460.26571440.24984539X-RAY DIFFRACTION100
2.46-2.590.27781400.23664530X-RAY DIFFRACTION100
2.59-2.750.27091500.24234553X-RAY DIFFRACTION100
2.75-2.960.27551410.2454547X-RAY DIFFRACTION100
2.96-3.250.24681370.21634557X-RAY DIFFRACTION100
3.25-3.720.23091450.1984569X-RAY DIFFRACTION100
3.72-4.680.16941490.16844574X-RAY DIFFRACTION100
4.68-19.590.21161530.18484633X-RAY DIFFRACTION99.98
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)
13.871352956410.767949329396-0.6062081386430.7047699536680.3266474525120.3025518684840.04558438883130.205237808844-0.08279814437950.00818950793039-0.1488523052880.813459424222-0.0977228707762-0.5255409309650.02415293084090.6294303060660.00871509658853-0.05649561028080.97713788317-0.03366945821571.53483828037-56.0233011592-4.14718498471-12.6474488141
21.74245687239-0.465658116967-0.3882143973633.872539058120.6647096370511.160945800920.07752938933380.2637605959620.0737757921587-0.895693893777-0.1242709785710.730102015954-0.185005508406-0.09028828149520.02426322242650.455419485310.0191285093538-0.164231126030.2666157367840.03716612491210.2385594198-14.10710411790.0169214333746-14.6825998453
31.6260601838-0.629413854559-0.6553228288543.572456371040.6617764859321.70656720341-0.06595039071550.214746425993-0.450926521351-0.387911520348-0.2298747130431.34704895490.160296229161-0.274497470631-0.1788659734440.265598264714-0.0141017990744-0.1433505920110.253835732054-0.08996473045960.588810617851-21.8443534397-12.7477107062-10.7995973415
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 190 )7 - 1901 - 165
22chain 'A' and (resid 191 through 587 )191 - 587166 - 561
33chain 'A' and (resid 588 through 839 )588 - 839562 - 813

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