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- PDB-3bne: Lipoxygenase-1 (Soybean) I553A Mutant -

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Basic information

Entry
Database: PDB / ID: 3bne
TitleLipoxygenase-1 (Soybean) I553A 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
: / Seed linoleate 13S-lipoxygenase-1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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)94,5362
Polymers94,4801
Non-polymers561
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.115, 92.951, 49.416
Angle α, β, γ (deg.)90.00, 90.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 94480.078 Da / Num. of mol.: 1 / Mutation: I553A, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
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: 1.4→31.4 Å / Num. all: 164852 / Num. obs: 164852 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.9
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 1.9 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1f8n

1f8n


Resolution: 1.4→29.72 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.918 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18603 5011 3 %RANDOM
Rwork0.16595 ---
obs0.16655 159804 100 %-
all-159804 --
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: 22.764 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.04 Å2
2---0.38 Å20 Å2
3---0.47 Å2
Refine analyzeLuzzati sigma a free: 0.038 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 1 692 7211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9649311
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84224.183306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.436151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9551537
X-RAY DIFFRACTIONr_chiral_restr0.110.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215232
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2690.23255
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.24789
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2574
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8851.54194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55426828
X-RAY DIFFRACTIONr_scbond_it2.41832638
X-RAY DIFFRACTIONr_scangle_it3.914.52483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.403→1.439 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 372 -
Rwork0.243 11074 -
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)
13.17970.4761-0.38361.86130.20642.21360.0560.276-0.0497-0.2869-0.1929-0.54430.04930.38160.1368-0.00240.00290.10110.07270.02740.312462.543844.29826.8872
21.9102-0.2622-0.56560.96610.00230.6790.0851-0.1216-0.0376-0.0341-0.0798-0.372-0.0420.1064-0.0053-0.0656-0.0219-0.01910.02190.02640.091346.533947.401317.2204
31.537-0.55160.1030.8046-0.39890.66830.05260.09260.3957-0.0231-0.0811-0.2748-0.17050.1130.02850.0359-0.00580.0094-0.00950.0250.011118.942960.5686-0.7344
40.90320.2182-0.30350.8468-0.1370.66110.0311-0.071-0.01660.1005-0.04450.0330.0014-0.07150.01340.0311-0.005-0.01360.0249-0.0032-0.03781.921940.084114.7256
51.0820.2149-0.10140.5484-0.02330.34170.0405-0.2119-0.18890.0453-0.0784-0.14850.02990.01950.0378-0.0119-0.0047-0.02320.01120.0562-0.006122.799636.258719.2549
61.0911-0.0553-0.04411.1632-0.26510.71050.01790.01220.0408-0.0168-0.01150.0142-0.0556-0.0894-0.00640.0536-0.0022-0.00550.03530.0006-0.019811.193248.44827.3883
71.70220.20120.32220.7234-0.05550.7575-0.01920.1531-0.3738-0.1379-0.0163-0.30130.11210.11250.03550.00350.02020.0554-0.0479-0.01450.057226.125929.55991.053
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 697 - 69
2X-RAY DIFFRACTION2AA70 - 24670 - 246
3X-RAY DIFFRACTION3AA247 - 318247 - 318
4X-RAY DIFFRACTION4AA319 - 457319 - 457
5X-RAY DIFFRACTION5AA458 - 677458 - 677
6X-RAY DIFFRACTION6AA678 - 766678 - 766
7X-RAY DIFFRACTION7AA767 - 839767 - 839

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