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- PDB-3fg3: Crystal structure of Delta413-417:GS I805W LOX -

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Basic information

Entry
Database: PDB / ID: 3fg3
TitleCrystal structure of Delta413-417:GS I805W LOX
ComponentsAllene oxide synthase-lipoxygenase protein
KeywordsOXIDOREDUCTASE / lipoxygenase / arichidonic metabolism / Dioxygenase / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Lyase / Membrane / Metal-binding / Multifunctional enzyme / Oxylipin biosynthesis
Function / homology
Function and homology information


arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / arachidonate metabolic process / oxylipin biosynthetic process / lipid oxidation / fatty acid biosynthetic process / iron ion binding / heme binding ...arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / arachidonate metabolic process / oxylipin biosynthetic process / lipid oxidation / fatty acid biosynthetic process / iron ion binding / heme binding / membrane / cytoplasm
Similarity search - Function
Lipoxygenase, mammalian / 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, mammalian / 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. / Catalase superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Allene oxide synthase-lipoxygenase protein
Similarity search - Component
Biological speciesPlexaura homomalla (black sea rod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsNeau, D.B. / Newcomer, M.E.
Citation
Journal: Biochemistry / Year: 2009
Title: The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.
Authors: Neau, D.B. / Gilbert, N.C. / Bartlett, S.G. / Boeglin, W. / Brash, A.R. / Newcomer, M.E.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Improving protein crystal quality by selective removal of a Ca(2+)-dependent membrane-insertion loop.
Authors: Neau, D.B. / Gilbert, N.C. / Bartlett, S.G. / Dassey, A. / Newcomer, M.E.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: Allene oxide synthase-lipoxygenase protein
B: Allene oxide synthase-lipoxygenase protein
C: Allene oxide synthase-lipoxygenase protein
D: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,00066
Polymers317,9284
Non-polymers4,07262
Water44,7672485
1
A: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,03824
Polymers79,4821
Non-polymers1,55623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,22212
Polymers79,4821
Non-polymers74011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,64219
Polymers79,4821
Non-polymers1,16018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09811
Polymers79,4821
Non-polymers61610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-43 kcal/mol
Surface area96250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.704, 170.214, 104.202
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Allene oxide synthase-lipoxygenase protein / Allene oxide synthase / Hydroperoxidehydrase / Arachidonate 8-lipoxygenase


Mass: 79482.039 Da / Num. of mol.: 4
Fragment: Arachidonate 8R-lipoxygenase: UNP residues 374-1066
Mutation: delta 413-417:GS, I805W
Source method: isolated from a genetically manipulated source
Details: lipoxygenase portion of an allen-oxide synthase/lipoxygenase fusion protein, expressed with an N-terminal His-Tag.
Source: (gene. exp.) Plexaura homomalla (black sea rod) / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O16025, arachidonate 8-lipoxygenase

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Non-polymers , 6 types, 2547 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2485 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS CLEARLY SEE ISOLEUCINES IN ELECTRON DENSITY INSTEAD OF VALINES PROVIDED IN THE DATABASE ...AUTHORS CLEARLY SEE ISOLEUCINES IN ELECTRON DENSITY INSTEAD OF VALINES PROVIDED IN THE DATABASE SEQUENCE. IT IS UNCLEAR WHETHER THESE DIFFERENCES REPRESENT SPONTANEOUS MUTATIONS OR AN ERROR IN THE DATABASE SEQUENCE.

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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: 2.88 Å3/Da / Density % sol: 57.23 %
Crystal growTemperature: 298 K / pH: 8
Details: 6-8% PEG 8000, 5% Glycerol, 0.2M CaCl2, 0.1M Imidazole acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 263905 / % possible obs: 96.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.576
Reflection shellResolution: 1.9→2.13 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / % possible all: 76.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0088phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3FG1

3fg1


Resolution: 1.9→34.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.834 / SU ML: 0.083 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 14029 5 %RANDOM
Rwork0.162 ---
obs0.164 263905 98.43 %-
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: 27.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å21.61 Å2
2---0.59 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21804 0 236 2485 24525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02223165
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.94231600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58952903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78824.5541196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.545153672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.23215122
X-RAY DIFFRACTIONr_chiral_restr0.1550.23338
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1971.513961
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.969222533
X-RAY DIFFRACTIONr_scbond_it3.25739204
X-RAY DIFFRACTIONr_scangle_it4.8264.58976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 1024 -
Rwork0.251 19291 -
obs--97.93 %

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