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- PDB-5eeo: soybean lipoxygenase(L1)-T756R -

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Basic information

Entry
Database: PDB / ID: 5eeo
Titlesoybean lipoxygenase(L1)-T756R
ComponentsSeed linoleate 13S-lipoxygenase-1
KeywordsOXIDOREDUCTASE
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-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 ...Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase-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, / Few Secondary Structures / Irregular / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Seed linoleate 13S-lipoxygenase-1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMikami, B. / Nagaya, T. / Hioki, Y.
CitationJournal: To Be Published
Title: The structural basis for specificity in lipoxygenase catalysis
Authors: Mikami, B. / Nagaya, T. / Hioki, Y.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.source / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)94,5922
Polymers94,5361
Non-polymers561
Water5,711317
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-14 kcal/mol
Surface area30860 Å2
Unit cell
Length a, b, c (Å)70.708, 62.361, 92.351
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 94536.219 Da / Num. of mol.: 1 / Mutation: Q104E, T756R
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-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium chloride, 20%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→38.7 Å / Num. all: 45418 / Num. obs: 45398 / % possible obs: 98.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 28.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 7.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8N

1f8n


Resolution: 2.1→38.7 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 2313 5.09 %
Rwork0.1857 --
obs0.1892 45398 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 1 317 6751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076753
X-RAY DIFFRACTIONf_angle_d1.1379190
X-RAY DIFFRACTIONf_dihedral_angle_d14.342530
X-RAY DIFFRACTIONf_chiral_restr0.081002
X-RAY DIFFRACTIONf_plane_restr0.0061193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.096-2.13870.32791210.22472323X-RAY DIFFRACTION90
2.1387-2.18520.29271190.21762551X-RAY DIFFRACTION100
2.1852-2.23610.26631290.20372562X-RAY DIFFRACTION100
2.2361-2.2920.30121330.20332536X-RAY DIFFRACTION99
2.292-2.3540.2591310.19442568X-RAY DIFFRACTION99
2.354-2.42320.30231430.19812532X-RAY DIFFRACTION99
2.4232-2.50140.28211170.2042555X-RAY DIFFRACTION99
2.5014-2.59080.25951390.20022482X-RAY DIFFRACTION98
2.5908-2.69450.30731430.20622517X-RAY DIFFRACTION97
2.6945-2.81710.31631440.2072469X-RAY DIFFRACTION97
2.8171-2.96560.27611590.20542469X-RAY DIFFRACTION97
2.9656-3.15130.29121440.21122549X-RAY DIFFRACTION99
3.1513-3.39450.26091300.19412542X-RAY DIFFRACTION99
3.3945-3.73580.24231240.17642572X-RAY DIFFRACTION99
3.7358-4.27580.21111520.15572580X-RAY DIFFRACTION100
4.2758-5.38480.18251430.14592596X-RAY DIFFRACTION100
5.3848-38.75340.22581420.17182683X-RAY DIFFRACTION100

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