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- PDB-1rrh: Soybean Lipoxygenase (LOX-3) at ambient temperatures at 2.0 A res... -

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Basic information

Entry
Database: PDB / ID: 1rrh
TitleSoybean Lipoxygenase (LOX-3) at ambient temperatures 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, 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 9S-lipoxygenase-3
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 / 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9752
Polymers96,9191
Non-polymers561
Water9,890549
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.709, 137.211, 61.792
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1377-

HOH

21A-1397-

HOH

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Components

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


Mass: 96919.000 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVARIANT RESIDUES IN STRAIN PROVAR ARE NOTED IN SWISS-PROT ENTRY P09186.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.84 %
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

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 15, 1997 / 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→99 Å / Num. all: 62944 / Num. obs: 54258 / % possible obs: 86.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.47 / Num. unique all: 4817 / % possible all: 0.767

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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→10 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.833 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.186 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.23059 2744 5.1 %RANDOM
Rwork0.17893 ---
all0.18155 62448 --
obs0.18155 53997 86.47 %-
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: 25.957 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20.88 Å2
2--0.66 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6789 0 1 549 7339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216967
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9549454
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395849
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_restr0.130.21033
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025331
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1580.073169
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.4734
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.0749
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.426
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0441.54243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77826878
X-RAY DIFFRACTIONr_scbond_it2.89832722
X-RAY DIFFRACTIONr_scangle_it4.3254.52576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 157
Rwork0.257 3231
Refinement TLS params.Method: refined / Origin x: 27.5134 Å / Origin y: 4.2078 Å / Origin z: 15.1744 Å
111213212223313233
T0.0152 Å20.0259 Å2-0.0291 Å2-0.0538 Å2-0.0501 Å2--0.0557 Å2
L0.9344 °20.3842 °2-0.3671 °2-1.3788 °2-0.3546 °2--1.4281 °2
S-0.0194 Å °0.037 Å °-0.0037 Å °0.0045 Å °0.0675 Å °0.1042 Å °0.0075 Å °-0.141 Å °-0.0481 Å °

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