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- PDB-1f8n: LIPOXYGENASE-1 (SOYBEAN) AT 100K, NEW REFINEMENT -

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Basic information

Entry
Database: PDB / ID: 1f8n
TitleLIPOXYGENASE-1 (SOYBEAN) AT 100K, NEW REFINEMENT
ComponentsLIPOXYGENASE-1
KeywordsOXIDOREDUCTASE / DIOXYGENASE / 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 / SYNCHROTRON / MIR / Resolution: 1.4 Å
AuthorsTomchick, D.R. / Minor, W. / Holman, T.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1.
Authors: Tomchick, D.R. / Phan, P. / Cymborowski, M. / Minor, W. / Holman, T.R.
#1: 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.
#2: Journal: CURR.OPIN.STRUCT.BIOL. / Year: 1994
Title: THE STRUCTURE AND FUNCTION OF LIPOXYGENASE
Authors: Nelson, M.J. / Seitz, S.P.
#3: Journal: J.Am.Chem.Soc. / Year: 1996
Title: EXPERIMENTAL EVIDENCE FOR EXTENSIVE TUNNELING OF HYDROGEN IN THE LIPOXYGENASE REACTION: IMPLICATIONS FOR ENZYME CATALYSIS
Authors: Jonsson, T. / Glickman, M.H. / Sun, S. / Klinman, J.P.
#4: Journal: Biochemistry / Year: 1995
Title: NATURE OF THE RATE-LIMITING STEPS IN THE SOYBEAN LIPOXYGENASE-1 REACTION
Authors: Glickman, M.H. / Klinman, J.P.
#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: 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 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 7, 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
Water16,177898
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


Mass: 94480.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: PT-7/L-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08170, 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.: 898 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5.6 / Details: Minor, W., (1996) Biochemistry, 35, 10687.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Macetate1drop
24 %(w/v)PEG34001drop
34 mg/mlprotein1drop
49 %PEG33501reservoir
50.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 161029 / Num. obs: 161029 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 35.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.343 / % possible all: 91.6
Reflection
*PLUS

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: val 312 has phi/psi values that are normally disallowed. val 312 is found in a tight turn between two beta strands, and the density is clear and strong.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 7559 5 %Random
Rwork0.198 ---
all0.205 151073 --
obs0.205 151073 88 %-
Solvent computationSolvent model: Anisotropic / Bsol: 54.134 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 23.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.356 Å20 Å20.569 Å2
2--1.817 Å20 Å2
3----3.173 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 1 898 7539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.4→1.45 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.314 566 3.3 %
Rwork0.285 11112 -
obs--68.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Rfactor Rfree: 0.314 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.285

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