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- PDB-4wfo: manganese-substituted soybean lipoxygenase-1 -

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Basic information

Entry
Database: PDB / ID: 4wfo
Titlemanganese-substituted soybean lipoxygenase-1
ComponentsSeed linoleate 13S-lipoxygenase-1
KeywordsOXIDOREDUCTASE / lipoxygenase / manganese / metal substitution
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
ACETATE ION / : / Seed linoleate 13S-lipoxygenase-1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsCarr, C.A.M. / Scouras, A.D. / Klinman, J.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM025765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008295 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM082250 United States
National Science Foundation (NSF, United States)CHE-0840505 United States
CitationJournal: To Be Published
Title: Direct detection of active-site geometries in soybean lipoxygenase-1 by ENDOR
Authors: Carr, C.A.M. / Horitani, M. / Offenbacher, A.R. / Knitz, M.W. / Klinman, J.P. / Hoffman, B.M.
History
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,68616
Polymers96,7811
Non-polymers90615
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.123, 91.497, 90.897
Angle α, β, γ (deg.)90.00, 93.88, 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: 96780.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: LOX1.1, LOX1 / Plasmid: pET / Details (production host): Addgene 29653 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus-RIL / References: UniProt: P08170, linoleate 13S-lipoxygenase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 9% PEG3350, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.14→90.69 Å / Num. obs: 268145 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.3
Reflection shellResolution: 1.14→1.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.7 / % possible all: 63.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZW

3pzw


Resolution: 1.14→90.689 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1277 1888 0.7 %
Rwork0.1077 --
obs0.1078 268091 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.14→90.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6579 0 57 1151 7787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097426
X-RAY DIFFRACTIONf_angle_d1.08310147
X-RAY DIFFRACTIONf_dihedral_angle_d13.0122814
X-RAY DIFFRACTIONf_chiral_restr0.0831089
X-RAY DIFFRACTIONf_plane_restr0.0091351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.17080.2628950.223514336X-RAY DIFFRACTION66
1.1708-1.20530.23381260.19617465X-RAY DIFFRACTION80
1.2053-1.24420.18481500.165620667X-RAY DIFFRACTION95
1.2442-1.28870.16741520.140920980X-RAY DIFFRACTION97
1.2887-1.34030.14091540.123521124X-RAY DIFFRACTION97
1.3403-1.40130.12511500.109821081X-RAY DIFFRACTION97
1.4013-1.47520.1351520.102221238X-RAY DIFFRACTION98
1.4752-1.56760.11511460.085921312X-RAY DIFFRACTION98
1.5676-1.68860.10051600.080121357X-RAY DIFFRACTION98
1.6886-1.85860.11071630.082121498X-RAY DIFFRACTION99
1.8586-2.12750.10871440.086221599X-RAY DIFFRACTION99
2.1275-2.68050.10361480.099921644X-RAY DIFFRACTION99
2.6805-90.97680.13321480.113621902X-RAY DIFFRACTION99

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