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- PDB-3bnc: Lipoxygenase-1 (Soybean) I553G Mutant -

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Basic information

Entry
Database: PDB / ID: 3bnc
TitleLipoxygenase-1 (Soybean) I553G Mutant
ComponentsSeed lipoxygenase-1
KeywordsOXIDOREDUCTASE / DIOXYGENASE / LIPOXYGENASE / METALLOPROTEIN / FATTY ACIDS / Fatty acid biosynthesis / Iron / Lipid synthesis / Metal-binding / Oxylipin biosynthesis / ----
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
ACETIC ACID / : / Seed linoleate 13S-lipoxygenase-1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsTomchick, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1.
Authors: Meyer, M.P. / Tomchick, D.R. / Klinman, J.P.
#1: Journal: Biochemistry / Year: 2003
Title: Kinetic studies of oxygen reactivity in soybean lipoxygenase-1.
Authors: Knapp, M.J. / Klinman, J.P.
History
DepositionDec 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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: Seed lipoxygenase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5823
Polymers94,4661
Non-polymers1162
Water14,430801
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.201, 92.278, 49.584
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Seed lipoxygenase-1 / L-1


Mass: 94466.055 Da / Num. of mol.: 1 / Mutation: I553G, S160E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: LOX1.1, LOX1 / Plasmid: PT-7/L-1 / 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
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: SBC-3 / Detector: CCD / Date: Sep 10, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.65→31.8 Å / Num. all: 102487 / Num. obs: 102487 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.5 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1f8n

1f8n


Resolution: 1.65→27.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.559 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20114 3067 3 %RANDOM
Rwork0.16928 ---
obs0.17026 98058 100 %-
all-98058 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.43 Å2
2---0.41 Å20 Å2
3---0.75 Å2
Refine analyzeLuzzati sigma a free: 0.063 Å
Refinement stepCycle: LAST / Resolution: 1.65→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 5 801 7354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226802
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9639257
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37924.137307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8911537
X-RAY DIFFRACTIONr_chiral_restr0.1080.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215209
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.23540
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24749
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8551.54173
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47426775
X-RAY DIFFRACTIONr_scbond_it2.44232629
X-RAY DIFFRACTIONr_scangle_it4.0154.52482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 217 -
Rwork0.26 6906 -
obs--100 %
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)
15.4413-2.44840.56961.83370.42970.75030.18990.68440.2665-0.1499-0.2855-0.1333-0.0870.05940.09560.04870.0160.0460.16210.06230.077762.653742.75511.0853
21.6835-0.3783-0.32120.8078-0.06310.73270.04020.04780.0196-0.0873-0.0454-0.14330.0080.15690.0051-0.0057-0.0068-0.00710.09330.00740.09157.973541.519811.9477
30.5538-0.11830.38310.0513-0.02820.3758-0.00060.00840.1404-0.0331-0.0193-0.091-0.09060.03610.01990.0197-0.01630.01390.01040.00840.022925.31558.303112.4781
40.68530.02660.02041.01390.13230.30680.00770.0014-0.0052-0.0019-0.0496-0.10170.0091-0.03380.0419-0.01720.0009-0.0066-0.0143-0.009-0.04928.284644.35086.8433
50.91040.45510.13742.35690.71941.28180.0609-0.13640.01480.2577-0.10680.1089-0.0286-0.09620.04590.055-0.02160.02280.0279-0.0047-0.0413-1.966538.579319.4631
63.53990.01530.1321.9386-0.15311.31230.0188-0.07340.19290.1118-0.04620.1465-0.0602-0.12640.02740.0867-0.00270.01840.059-0.01420.0207-0.833746.557214.2605
70.99950.05070.09840.32290.04480.32080.0253-0.11360.03610.026-0.0229-0.0279-0.0234-0.0084-0.00230.0291-0.0132-0.00870.03670.02260.008226.328242.110419.3192
81.1393-0.09420.18350.4374-0.05250.5750.0531-0.1755-0.29080.0849-0.0346-0.06790.12250.0335-0.01860.056-0.0033-0.0160.03690.06360.089228.542527.335919.8876
91.0003-0.2262-0.17681.2565-0.05980.91360.02120.04330.10220.02-0.01510.0607-0.0922-0.1208-0.00610.0557-0.00540.00210.03460.0056-0.00868.373851.45186.0001
101.7517-0.08450.39090.44190.05710.64880.060.1588-0.2402-0.0466-0.0446-0.12820.11280.0951-0.01540.04780.01620.02260.0208-0.01220.058625.407529.74030.8653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 331 - 33
2X-RAY DIFFRACTION2AA34 - 17834 - 178
3X-RAY DIFFRACTION3AA179 - 312179 - 312
4X-RAY DIFFRACTION4AA313 - 377313 - 377
5X-RAY DIFFRACTION5AA378 - 457378 - 457
6X-RAY DIFFRACTION6AA458 - 499458 - 499
7X-RAY DIFFRACTION7AA500 - 591500 - 591
8X-RAY DIFFRACTION8AA592 - 697592 - 697
9X-RAY DIFFRACTION9AA698 - 768698 - 768
10X-RAY DIFFRACTION10AA769 - 839769 - 839

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