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- PDB-7soj: Structure of V750A Soybean Lipoxygenase at 277K -

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Basic information

Entry
Database: PDB / ID: 7soj
TitleStructure of V750A Soybean Lipoxygenase at 277K
ComponentsLipoxygenase
KeywordsOXIDOREDUCTASE / metal binding / lipid binding
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxylipin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily ...Lipoxygenase, plant / Lipoxygenase, domain 3 / Plant lipoxygenase, PLAT/LH2 domain / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 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.
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsGee, C.L. / Offenbacher, A.R. / Hu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118117 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase.
Authors: Zaragoza, J.P.T. / Offenbacher, A.R. / Hu, S. / Gee, C.L. / Firestein, Z.M. / Minnetian, N. / Deng, Z. / Fan, F. / Iavarone, A.T. / Klinman, J.P.
History
DepositionOct 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: Lipoxygenase
B: Lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,1004
Polymers188,9882
Non-polymers1122
Water16,826934
1
A: Lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5502
Polymers94,4941
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5502
Polymers94,4941
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.537, 92.693, 100.270
Angle α, β, γ (deg.)90.000, 93.754, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Lipoxygenase /


Mass: 94494.102 Da / Num. of mol.: 2 / Mutation: V750A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3TDK4, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 934 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 acetate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1.85→46.35 Å / Num. obs: 141110 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.092 / Net I/σ(I): 5.7
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 2.46 / Num. unique obs: 6896 / CC1/2: 0.469 / Rpim(I) all: 1.57

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5t5v

5t5v


Resolution: 1.85→46.35 Å / SU ML: 0.2301 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1984 6993 4.96 %
Rwork0.1685 133906 -
obs0.17 140899 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.25 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13075 0 2 934 14011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004613931
X-RAY DIFFRACTIONf_angle_d0.819718997
X-RAY DIFFRACTIONf_chiral_restr0.04592083
X-RAY DIFFRACTIONf_plane_restr0.00752475
X-RAY DIFFRACTIONf_dihedral_angle_d13.66775236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.40422290.35754417X-RAY DIFFRACTION98.14
1.87-1.890.32852510.32564394X-RAY DIFFRACTION98.14
1.89-1.920.31692190.28694412X-RAY DIFFRACTION98.2
1.92-1.940.27632520.27224362X-RAY DIFFRACTION98.38
1.94-1.970.28492620.26084411X-RAY DIFFRACTION98.32
1.97-1.990.27021940.2464467X-RAY DIFFRACTION98.52
1.99-2.020.26872170.23484418X-RAY DIFFRACTION98.43
2.02-2.050.26112220.23294461X-RAY DIFFRACTION98.61
2.05-2.080.24172250.22884458X-RAY DIFFRACTION98.65
2.08-2.120.26232060.22844407X-RAY DIFFRACTION98.51
2.12-2.150.25592210.21414475X-RAY DIFFRACTION98.61
2.15-2.190.23592210.20294451X-RAY DIFFRACTION98.71
2.19-2.240.24172150.19454506X-RAY DIFFRACTION98.91
2.24-2.280.22642490.18784421X-RAY DIFFRACTION98.79
2.28-2.330.21032330.17854463X-RAY DIFFRACTION99.01
2.33-2.390.24452220.17864446X-RAY DIFFRACTION99.02
2.39-2.440.22542270.17914492X-RAY DIFFRACTION98.99
2.44-2.510.21612440.17144445X-RAY DIFFRACTION98.9
2.51-2.580.20392420.174435X-RAY DIFFRACTION99.03
2.58-2.670.23082440.17444455X-RAY DIFFRACTION99.16
2.67-2.760.20492350.17724483X-RAY DIFFRACTION99.28
2.76-2.870.22432470.174481X-RAY DIFFRACTION99.41
2.87-30.18312670.16634429X-RAY DIFFRACTION99.41
3-3.160.19792630.16384513X-RAY DIFFRACTION99.5
3.16-3.360.19052070.15694525X-RAY DIFFRACTION99.56
3.36-3.620.17832130.13844530X-RAY DIFFRACTION99.6
3.62-3.980.14832560.11824513X-RAY DIFFRACTION99.62
3.98-4.560.12722290.11054552X-RAY DIFFRACTION99.71
4.56-5.740.12332500.1164525X-RAY DIFFRACTION99.71
5.75-46.350.18252310.14954559X-RAY DIFFRACTION97.74

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