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- PDB-4qwt: Anaerobic crystal structure of delta413-417:GS LOX in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4qwt
TitleAnaerobic crystal structure of delta413-417:GS LOX in complex with arachidonate
ComponentsAllene oxide synthase-lipoxygenase protein
KeywordsOXIDOREDUCTASE / iron binding / membrane-associated
Function / homology
Function and homology information


arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid metabolic 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 / oxylipin biosynthetic process / arachidonic acid metabolic 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
ARACHIDONIC ACID / ACETATE ION / : / Allene oxide synthase-lipoxygenase protein
Similarity search - Component
Biological speciesPlexaura homomalla (black sea rod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsNeau, D.B. / Newcomer, M.E.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of a Lipoxygenase in Complex with Substrate: THE ARACHIDONIC ACID-BINDING SITE OF 8R-LIPOXYGENASE.
Authors: Neau, D.B. / Bender, G. / Boeglin, W.E. / Bartlett, S.G. / Brash, A.R. / Newcomer, M.E.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Sep 20, 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_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_asym_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

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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)321,73965
Polymers317,6364
Non-polymers4,10361
Water32,3371795
1
A: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,64821
Polymers79,4091
Non-polymers1,23920
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,23713
Polymers79,4091
Non-polymers82812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,77519
Polymers79,4091
Non-polymers1,36618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,07912
Polymers79,4091
Non-polymers67011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.030, 170.670, 104.720
Angle α, β, γ (deg.)90.00, 95.36, 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 / Arachidonate 8-lipoxygenase


Mass: 79408.992 Da / Num. of mol.: 4 / Fragment: lipoxygenase domain (UNP residues 374-1066) / Mutation: delta413-417:GS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plexaura homomalla (black sea rod) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O16025, arachidonate 8-lipoxygenase

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Non-polymers , 7 types, 1856 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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-ACD / ARACHIDONIC ACID / Arachidonic acid


Mass: 304.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1795 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 6-8% PEG8000, 5% glycerol, 0.2 M calcium chloride, 0.1 M imidazole acetate, pH 8.0, anaerobic, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2010 / Details: mirrors
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 243605 / Num. obs: 242387 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.102 / Rsym value: 0.119 / Net I/σ(I): 11.68
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.951 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GF1

3gf1


Resolution: 2.002→48.416 Å / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / σ(F): 1.34 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1988 0.82 %
Rwork0.1618 --
obs0.1622 242312 99.46 %
all-243664 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.32 Å2
Refinement stepCycle: LAST / Resolution: 2.002→48.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21517 0 242 1795 23554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722643
X-RAY DIFFRACTIONf_angle_d0.98130866
X-RAY DIFFRACTIONf_dihedral_angle_d13.1688148
X-RAY DIFFRACTIONf_chiral_restr0.0423282
X-RAY DIFFRACTIONf_plane_restr0.0054082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0021-2.05210.31661340.273816206X-RAY DIFFRACTION95
2.0521-2.10760.28791390.236617220X-RAY DIFFRACTION100
2.1076-2.16960.2731440.217417207X-RAY DIFFRACTION100
2.1696-2.23970.24171490.204317136X-RAY DIFFRACTION100
2.2397-2.31970.31191390.195217221X-RAY DIFFRACTION100
2.3197-2.41260.22211410.186917233X-RAY DIFFRACTION100
2.4126-2.52240.26691390.185617176X-RAY DIFFRACTION100
2.5224-2.65530.21661440.169517261X-RAY DIFFRACTION100
2.6553-2.82170.20091420.16517244X-RAY DIFFRACTION100
2.8217-3.03950.20661460.161217250X-RAY DIFFRACTION100
3.0395-3.34530.23211410.156417231X-RAY DIFFRACTION100
3.3453-3.82930.1791460.141617240X-RAY DIFFRACTION100
3.8293-4.82380.16371400.118217329X-RAY DIFFRACTION100
4.8238-48.42990.20241440.143517370X-RAY DIFFRACTION99

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