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- PDB-3bnb: Lipoxygenase-1 (Soybean) I553L Mutant -

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Basic information

Entry
Database: PDB / ID: 3bnb
TitleLipoxygenase-1 (Soybean) I553L 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: 1.45 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)94,5782
Polymers94,5221
Non-polymers561
Water13,295738
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.421, 92.726, 49.416
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 94522.156 Da / Num. of mol.: 1 / Mutation: I553L, 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.: 738 / 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: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG3350, SODIUM ACETATE, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00686 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: 1.00686 Å / Relative weight: 1
ReflectionResolution: 1.45→42.1 Å / Num. all: 144404 / Num. obs: 144404 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 26.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.1 / % possible all: 85.2

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Processing

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

1f8n


Resolution: 1.45→29.37 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.06 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18684 4381 3 %RANDOM
Rwork0.16618 ---
obs0.16682 139850 100 %-
all-139850 --
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: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.2 Å2
2---0.64 Å20 Å2
3---0.87 Å2
Refine analyzeLuzzati sigma a obs: 0.041 Å
Refinement stepCycle: LAST / Resolution: 1.45→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 1 738 7257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9639248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0945838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08524.137307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.271151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1681537
X-RAY DIFFRACTIONr_chiral_restr0.1170.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215196
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.23235
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24704
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2519
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9071.54158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52826761
X-RAY DIFFRACTIONr_scbond_it2.50232634
X-RAY DIFFRACTIONr_scangle_it3.9134.52487
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 290 -
Rwork0.207 9202 -
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)
11.8543-0.1692-0.37230.86490.06120.58330.0922-0.0356-0.0336-0.0429-0.0476-0.3825-0.02680.1341-0.04450.0298-0.0204-0.0150.07690.00130.172650.259546.534214.7541
21.9941-0.2198-0.06140.6722-0.34650.66730.06730.07210.3847-0.0133-0.0741-0.1869-0.16640.06980.00680.0514-0.00910.00780.00620.03490.01918.543360.6772-0.8044
30.92850.176-0.06580.83770.11510.27130.0276-0.0465-0.05330.0931-0.04890.03750.0528-0.09540.02130.0526-0.0134-0.00180.0418-0.0065-0.03562.66138.285813.1964
41.42370.2978-0.17051.37050.04970.86960.0571-0.11090.15040.1468-0.07250.1402-0.0558-0.12940.01530.0706-0.00910.01230.0747-0.0092-0.0158-0.1344.875216.7116
51.36810.2154-0.09710.48360.00220.38960.0548-0.1698-0.14180.0561-0.0534-0.13080.0277-0.0044-0.00140.034-0.0099-0.02950.03550.0344025.803839.862918.9065
61.08810.15990.00670.6927-0.10140.47940.021-0.0378-0.19820.0092-0.035-0.15360.04470.00650.0140.0425-0.00490.00050.01160.01410.015722.407135.474510.2975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 2466 - 246
2X-RAY DIFFRACTION2AA247 - 318247 - 318
3X-RAY DIFFRACTION3AA319 - 415319 - 415
4X-RAY DIFFRACTION4AA416 - 499416 - 499
5X-RAY DIFFRACTION5AA500 - 601500 - 601
6X-RAY DIFFRACTION6AA602 - 839602 - 839

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