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- PDB-1u5u: The structure of an Allene Oxide Synthase reveals a novel use for... -

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Basic information

Entry
Database: PDB / ID: 1u5u
TitleThe structure of an Allene Oxide Synthase reveals a novel use for a catalase fold
ComponentsAllene oxide synthase-lipoxygenase protein
KeywordsLYASE / ALLENE OXIDE SYNTHASE / CATALASE / HEME / EICOSANOID / FUSION PROTEIN
Function / homology
Function and homology information


arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / lipoxygenase pathway / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process ...arachidonate 8-lipoxygenase / arachidonate 8(R)-lipoxygenase activity / allene oxide synthase activity / lipoxygenase pathway / Lyases; Carbon-oxygen lyases; Hydro-lyases / oxylipin biosynthetic process / arachidonic acid metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / iron ion binding / heme binding / membrane / cytoplasm
Similarity search - Function
Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. ...Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 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 HpII, Chain A, domain 1 / Catalase core domain / Catalase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Allene oxide synthase-lipoxygenase protein
Similarity search - Component
Biological speciesPlexaura homomalla (black sea rod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsOldham, M.L. / Brash, A.R. / Newcomer, M.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The structure of coral allene oxide synthase reveals a catalase adapted for metabolism of a fatty acid hydroperoxide.
Authors: Oldham, M.L. / Brash, A.R. / Newcomer, M.E.
History
DepositionJul 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0634
Polymers85,8302
Non-polymers1,2332
Water10,251569
1
A: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5322
Polymers42,9151
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5322
Polymers42,9151
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-64 kcal/mol
Surface area30260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.940, 76.679, 77.761
Angle α, β, γ (deg.)90.00, 109.66, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer

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Components

#1: Protein Allene oxide synthase-lipoxygenase protein


Mass: 42915.215 Da / Num. of mol.: 2 / Fragment: Allene Oxide Synthase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plexaura homomalla (black sea rod) / Plasmid: pET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O16025, hydroperoxide dehydratase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 298 K / pH: 5.7
Details: PEG MME 5000, bis-tris, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 5.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.7346
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2004
RadiationMonochromator: SI (111) CHANNEL-CUT MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7346 Å / Relative weight: 1
ReflectionResolution: 2→34.83 Å / Num. obs: 104610 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 11.6 Å2 / Rsym value: 0.082 / Net I/σ(I): 21.5
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.362 / % possible all: 88

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→34.83 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1354 1.3 %RANDOM
Rwork0.196 ---
all0.209 104060 --
obs0.209 104060 95.6 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 44.08 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 20.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å22.71 Å2-2.02 Å2
2--0 Å2-2.44 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 86 569 6621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.282 155 1.3 %
Rwork0.246 11635 -
obs--86.3 %

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