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- PDB-1yge: LIPOXYGENASE-1 (SOYBEAN) AT 100K -

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Basic information

Entry
Database: PDB / ID: 1yge
TitleLIPOXYGENASE-1 (SOYBEAN) AT 100K
ComponentsLIPOXYGENASE-1
KeywordsDIOXYGENASE / LIPOXYGENASE / METALLOPROTEIN / FATTY ACIDS
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 / Resolution: 1.4 Å
AuthorsMinor, W. / Steczko, J. / Stec, B. / Otwinowski, Z. / Bolin, J.T. / Walter, R. / Axelrod, B.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of soybean lipoxygenase L-1 at 1.4 A resolution.
Authors: Minor, W. / Steczko, J. / Stec, B. / Otwinowski, Z. / Bolin, J.T. / Walter, R. / Axelrod, B.
#1: Journal: Biochemistry / Year: 1994
Title: Position 713 is Critical for Catalysis But not Iron Binding in Soybean Lipoxygenase
Authors: Kramer, J.A. / Johnson, K.R. / Dunham, W.R. / Sands, R.H. / Funk Junior, M.O.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1994
Title: The Structure and Function of Lipoxygenase
Authors: Nelson, M.J. / Seitz, S.P.
#3: Journal: Biochemistry / Year: 1994
Title: Structural Characterization of Alkyl and Peroxyl Radicals in Solutions of Purple Lipoxygenase
Authors: Nelson, M.J. / Cowling, R.A. / Seitz, S.P.
#4: Journal: Biochemistry / Year: 1994
Title: X-Ray Spectroscopy of the Iron Site in Soybean Lipoxygenase-1: Changes in Coordination Upon Oxidation or Addition of Methanol
Authors: Scarrow, R.C. / Trimitsis, M.G. / Buck, C.P. / Grove, G.N. / Cowling, R.A. / Nelson, M.J.
#5: Journal: Science / Year: 1993
Title: The Three-Dimensional Structure of an Arachidonic Acid 15-Lipoxygenase
Authors: Boyington, J.C. / Gaffney, B.J. / Amzel, L.M.
#6: Journal: Biochemistry / Year: 1993
Title: Crystallographic Determination of the Active Site Iron and its Ligands in Soybean Lipoxygenase L-1
Authors: Minor, W. / Steczko, J. / Bolin, J.T. / Otwinowski, Z. / Axelrod, B.
#7: Journal: Biochemistry / Year: 1992
Title: Conserved Histidine Residues in Soybean Lipoxygenase: Functional Consequences of Their Replacement
Authors: Steczko, J. / Donoho, G.P. / Clemens, J.C. / Dixon, J.E. / Axelrod, B.
#8: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Spectroscopic Studies of the Non-Heme Ferric Active Site in Soybean Lipoxygenase: Magnetic Circular Dichroism as a Probe of Electronic and Geometric Structure. Ligand-Field Origin of Zero-Field
Authors: Zhang, Y. / Gebhard, M.S. / Solomon, E.I.
#9: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization and Preliminary X-Ray Investigation of Lipoxygenase 1 from Soybeans
Authors: Steczko, J. / Muchmore, C.R. / Smith, J.L. / Axelrod, B.
History
DepositionJun 4, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIPOXYGENASE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5362
Polymers94,4801
Non-polymers561
Water27,1671508
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.900, 94.000, 49.900
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LIPOXYGENASE-1 / / L-1


Mass: 94480.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / References: UniProt: P08170, linoleate 13S-lipoxygenase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1508 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Macetate1drop
24 %(w/v)PEG34001drop
34-5 mg/mlenzyme1drop
48 %(w/v)PEG34001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Apr 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 161029 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 40 Å / Num. all: 169235
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å / % possible obs: 92 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
X-PLOR3.1phasing
RefinementResolution: 1.4→10 Å / σ(F): 2
Details: THE ELECTRON DENSITY FOR RESIDUES 1 - 6 IS WEAK AND FRAGMENTED SUGGESTING THAT THIS IS A MOBILE SEGMENT. FOR RESIDUES 22 - 30, WHICH FORM PART OF AN EXTENDED LOOP, THE DENSITY INDICATES THE ...Details: THE ELECTRON DENSITY FOR RESIDUES 1 - 6 IS WEAK AND FRAGMENTED SUGGESTING THAT THIS IS A MOBILE SEGMENT. FOR RESIDUES 22 - 30, WHICH FORM PART OF AN EXTENDED LOOP, THE DENSITY INDICATES THE COURSE OF THE POLYPEPTIDE AND THE LOCATION OF THE SIDE CHAINS, BUT IS NOT FULLY CONTINUOUS. TWO ADDITIONAL LOOPS, COMPRISING RESIDUES 70 - 73 AND 116 - 120, ARE REPRESENTED BY CONTINUOUS, BUT LESS THAN DEFINITE DENSITY. ALL FOUR SEGMENTS ARE INCLUDED IN THE CURRENT MODEL.
RfactorNum. reflection
Rfree0.243 -
Rwork0.197 -
obs0.197 136841
Displacement parametersBiso mean: 17.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6665 0 1 1377 8043
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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