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- PDB-1rrl: Soybean Lipoxygenase (LOX-3) at 93K at 2.0 A resolution -

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Basic information

Entry
Database: PDB / ID: 1rrl
TitleSoybean Lipoxygenase (LOX-3) at 93K at 2.0 A resolution
ComponentsSeed lipoxygenase-3
KeywordsOXIDOREDUCTASE / iron metalloprotein / lipoxygenase
Function / homology
Function and homology information


linoleate 9S-lipoxygenase / linoleate 9S-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 biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase-1 / Lipoxygenase, plant ...Lipoxygenase-1; domain 3 / Lipoxygenase-1; Domain 3 / Lipoxygenase-1; domain 2 / Lipoxygenase-1; Domain 2 / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / PLAT/LH2 domain / Lipoxygenase-1 / 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. / 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 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBorbulevych, O.Y. / Jankun, J. / Skrzypczak-Jankun, E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.
Authors: Skrzypczak-Jankun, E. / BORBULEVYCH, O.Y. / ZAVODSZKY, M.I. / BARANSKI, M.R. / PADMANABHAN, K. / PETRICEK, V. / JANKUN, J.
#1: Journal: Proteins / Year: 1997
Title: Structure of soybean lipoxygenase L3 and a comparison with its L1 isoenzyme
Authors: Skrzypczak-Jankun, E. / Amzel, L.M. / Kroa, B. / Funk, M.O.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Flash-freezing causes a stress induced modulation in a crystal structure of soybean lipoxygenase L3
Authors: Skrzypczak-Jankun, E. / Bianchet, M. / Amzel, L.M. / Funk, M.O.
History
DepositionDec 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seed lipoxygenase-3
B: Seed lipoxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9504
Polymers193,8382
Non-polymers1122
Water19,1501063
1
A: Seed lipoxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9752
Polymers96,9191
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Seed lipoxygenase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9752
Polymers96,9191
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.400, 133.500, 60.700
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Seed lipoxygenase-3 / L-3


Mass: 96919.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Strain: Soybean Provar cultivar / References: UniProt: P09186, linoleate 13S-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 1063 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVARIANT RESIDUES IN STRAIN PROVAR ARE NOTED IN SWISS-PROT ENTRY P09186. THE SEQUENCE FOR SOYBEAN ...VARIANT RESIDUES IN STRAIN PROVAR ARE NOTED IN SWISS-PROT ENTRY P09186. THE SEQUENCE FOR SOYBEAN LIPOXYGENASE L3 IS FROM PROVAR CULTIVAR AS PUBLISHED IN KRAMER ET AL., 1994, BIOCHEMISTRY, 33, 15017-15022 (PUBMED 7999759) AND THE DNA SEQUENCE IS DEPOSITED IN GENBANK (1236629, U50081).

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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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 20% PEG 8000, citrate-phosphate buffer 0.05M, tris.HCl, 0.2% sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 5.30

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 15, 1995 / Details: graphite monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→60 Å / Num. obs: 65033 / % possible obs: 64.5 % / Observed criterion σ(I): 0.25 / Redundancy: 2 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.4 / % possible all: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
bioteXdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NO3

1no3


Resolution: 2.09→10 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.366 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.258 / ESU R Free: 0.366 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.305 3245 5.1 %RANDOM
Rwork0.207 ---
obs0.212 64208 65.4 %-
all-98133 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20.64 Å2
2--1.93 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.09→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13578 0 2 1063 14643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02113936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2071.95418908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74651698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1460.22066
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0210662
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1790.0727680
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.51444
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.072150
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.545
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0611.58486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.768213756
X-RAY DIFFRACTIONr_scbond_it3.24335444
X-RAY DIFFRACTIONr_scangle_it4.5994.55152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.387 119
Rwork0.345 1972
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)
11.4760.1884-0.61971.7771-0.7371.3740.07830.1456-0.0187-0.1058-0.03770.0751-0.01-0.091-0.04070.10270.0484-0.02360.1482-0.06290.072449.6610.051715.2438
21.2563-0.1441-0.54091.78690.72791.43280.0852-0.129-0.01590.1111-0.007-0.104-0.03260.0693-0.07820.11-0.038-0.03250.07030.06230.0664-0.83750.0462-14.1418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 857
2X-RAY DIFFRACTION2B8 - 857

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