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- PDB-3dy5: Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla -

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Basic information

Entry
Database: PDB / ID: 3dy5
TitleAllene oxide synthase 8R-lipoxygenase from Plexaura homomalla
ComponentsAllene oxide synthase-lipoxygenase protein
KeywordsLYASE / OXIDOREDUCTASE / fusion protein / bi-functional enzyme / Dioxygenase / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / 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 / 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-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal ...Lipoxygenase, mammalian / Lipoxygenase-1; domain 5 / Lipoxygenase-1; Domain 5 / Nuclear Transport Factor 2; Chain: A, - #60 / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha / Alpha 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 / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsGilbert, N.C. / Niebuhr, M. / Tsuruta, H. / Newcomer, M.E.
CitationJournal: Biochemistry / Year: 2008
Title: A covalent linker allows for membrane targeting of an oxylipin biosynthetic complex.
Authors: Gilbert, N.C. / Niebuhr, M. / Tsuruta, H. / Bordelon, T. / Ridderbusch, O. / Dassey, A. / Brash, A.R. / Bartlett, S.G. / Newcomer, M.E.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim
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_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_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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
C: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,2846
Polymers243,9402
Non-polymers1,3454
Water00
1
A: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6423
Polymers121,9701
Non-polymers6722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Allene oxide synthase-lipoxygenase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6423
Polymers121,9701
Non-polymers6722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)235.520, 77.493, 157.966
Angle α, β, γ (deg.)90.00, 112.45, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 3 - 1066 / Label seq-ID: 3 - 1066

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CB

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Components

#1: Protein Allene oxide synthase-lipoxygenase protein / [Includes: Allene oxide synthase (EC 4.2.1.92) (Hydroperoxidehydrase) / and Arachidonate 8- ...[Includes: Allene oxide synthase (EC 4.2.1.92) (Hydroperoxidehydrase) / and Arachidonate 8-lipoxygenase (EC 1.13.11.40)]


Mass: 121969.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plexaura homomalla (black sea rod) / Plasmid: pTBfusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O16025, hydroperoxide dehydratase, arachidonate 8-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Sequence detailsAUTHORS STATE THAT IT MAY BE AN ERROR IN THE SEQUENCE DATABASE SINCE THERE IS CLEARLY ILE AT THAT ...AUTHORS STATE THAT IT MAY BE AN ERROR IN THE SEQUENCE DATABASE SINCE THERE IS CLEARLY ILE AT THAT POSITION ACCORDING TO ELECTRON DENSITY IN THIS AND ALL RELATED ENTRIES.

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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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The drops were prepared with 2:1:1 mixtures of protein (5 mg/mL in 4 mM CaCl2), detergent (1.8 mM Triton X-100), and precipitant (16% PEG 3350, 4% Tacsimate pH 6.0), VAPOR DIFFUSION, HANGING ...Details: The drops were prepared with 2:1:1 mixtures of protein (5 mg/mL in 4 mM CaCl2), detergent (1.8 mM Triton X-100), and precipitant (16% PEG 3350, 4% Tacsimate pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 3.5→39.2 Å / Num. obs: 32748 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.135
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 1.84 / Num. unique all: 2833 / % possible all: 86.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2FNQ, 1U5U

2fnq

1u5u


Resolution: 3.51→20.86 Å / Cor.coef. Fo:Fc: 0.848 / Cor.coef. Fo:Fc free: 0.792 / SU B: 108.329 / SU ML: 0.734 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.837 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32191 1644 5 %RANDOM
Rwork0.27264 ---
obs0.27513 30961 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 2.001 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å2-4.14 Å2
2---0.56 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 3.51→20.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16130 0 88 0 16218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02216644
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.96722592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50951990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53224.251828
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.552152782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6711598
X-RAY DIFFRACTIONr_chiral_restr0.0820.22382
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212880
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.28142
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.211051
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2622
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3490.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.510258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0216114
X-RAY DIFFRACTIONr_scbond_it037344
X-RAY DIFFRACTIONr_scangle_it04.56474
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8108 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal00.5
LS refinement shellResolution: 3.51→3.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 95 -
Rwork0.34 1861 -
obs--82.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1736-0.2380.70393.26850.41423.49990.23740.168-0.2585-0.0248-0.359-0.22850.3790.08880.12160.1552-0.0003-0.1239-0.0014-0.1097-0.043744.5333-77.7194-42.2131
23.240.4170.31442.94810.76942.5325-0.40550.46850.6022-0.10870.05370.1039-0.3654-0.17620.3518-0.0669-0.1724-0.0121-0.10720.24060.029-11.9085-35.8949-60.2001
33.30041.27830.87313.1371-0.08273.1679-0.08390.2762-0.2593-0.350.0001-0.24820.21850.31060.08390.00270.1201-0.0773-0.1891-0.1452-0.1640.5964-86.338-50.0209
46.8515-1.97212.04028.4483-1.29831.3420.5540.40030.1725-0.5925-0.17040.9329-0.6185-0.0541-0.38370.34870.3318-0.2689-0.2805-0.196-0.339631.3022-72.1847-45.6386
56.53732.17360.31183.9199-0.20162.2753-0.54590.89780.6865-0.62840.2780.157-0.36950.1640.2679-0.0283-0.1039-0.124-0.24230.2393-0.028-4.1992-27.272-64.3188
63.91122.20343.27852.55590.51254.1029-0.0672-0.5851-0.35310.29730.5828-0.33010.641.0146-0.5155-0.0691-0.06630.0338-0.27070.20920.04770.887-41.4271-55.3942
75.33532.5259-1.89983.3615-0.165619.0247-0.01040.4754-0.2628-0.4697-0.38360.5261-0.6555-0.08550.3939-0.10870.0696-0.0482-0.26450.04730.089824.628-45.5135-51.1702
88.36021.7794-7.36718.89996.128221.2729-0.0746-0.18910.4428-0.157-0.2787-0.30380.64360.03070.3533-0.1455-0.08990.0188-0.16360.00130.12749.5379-68.0948-56.0909
92.2160.93041.933.81641.97016.77660.05880.22370.1985-0.7028-0.03150.6261-0.36880.016-0.0273-0.0483-0.0025-0.1938-0.23720.0575-0.030731.3478-40.491-43.0645
105.79143.184-2.61585.6839-1.80522.8138-0.10380.0214-0.4640.0915-0.1503-1.31710.26880.28450.2541-0.13390.11510.0054-0.309-0.05030.1643-0.6204-73.1222-53.3275
1138.6785-9.96-48.405831.10236.522782.0542-0.2728-2.3963-2.8484-2.1821-3.45820.0523-2.88850.49953.7310.0555-0.1714-0.230.02720.25740.077918.1069-44.4086-19.1777
125.7573-7.61314.979512.7416-23.5111.2907-0.08110.2225-1.77380.1459-0.523-1.7581-0.54932.7790.6041-0.0051-0.17470.1781-0.008-0.17770.1206-3.5345-69.216-26.1719
137.6982-2.25810.82913.1523-1.22376.7907-0.2750.15220.05610.43580.22110.0949-0.37140.37650.054-0.0475-0.16320.05010.0585-0.1421-0.339942.5566-41.32248.6695
144.4011-1.53332.00765.97770.32986.4646-0.0174-0.3888-0.49270.3490.0865-0.30411.0066-0.5272-0.06910.1437-0.38380.03190.06840.0894-0.2934-39.5544-72.3186-17.4568
150.34170.8370.04222.787-0.85616.9213-0.1091-0.1990.44870.08720.06710.2046-0.44490.19760.042-0.2791-0.107-0.0147-0.1232-0.1242-0.227340.1269-39.1636-15.2495
161.8613-1.3479-2.74194.66920.88264.3686-0.0914-0.2089-0.48240.7547-0.0646-0.02530.6370.13510.156-0.1142-0.2102-0.0867-0.16430.08-0.3258-23.8041-74.4648-35.6253
172.66543.86572.04666.40130.57818.759-0.07950.06360.5723-0.6382-0.5199-0.3554-0.44990.86070.5994-0.1062-0.0155-0.1355-0.13930.0433-0.280951.2483-37.8766-29.3451
184.34510.75680.74594.41761.71865.85790.26780.4367-0.4175-0.4843-0.32910.2280.7591-0.66940.0614-0.3105-0.12060.1628-0.17360.006-0.4048-24.7907-75.7449-53.5524
191.0625-1.4111-1.80413.57653.17693.7613-0.1139-0.13390.21580.61150.09940.34230.7635-0.40830.0145-0.02440.0246-0.1133-0.05480.03350.018933.2262-47.7597-12.4631
203.31952.8636-3.32665.6323-5.41856.28970.4648-0.8068-0.15651.153-0.3205-0.2452-0.68090.7631-0.14440.1730.0131-0.2053-0.2066-0.0225-0.023-19.7657-65.8697-29.3739
210.17440.0586-0.56122.6723-5.043310.69090.40850.3538-0.4954-0.05040.22470.03520.77030.9333-0.6332-0.0523-0.0789-0.1039-0.1586-0.126-0.157739.2944-59.1989-13.5297
221.0499-2.6273-2.16316.63874.88028.8945-0.3159-0.03721.02670.663-0.4034-0.678-0.0298-0.43710.7193-0.1599-0.22390.0333-0.29420.2081-0.3229-24.1195-54.4302-33.7317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 833 - 83
2X-RAY DIFFRACTION2CB3 - 833 - 83
3X-RAY DIFFRACTION3AA84 - 32084 - 320
4X-RAY DIFFRACTION4AA321 - 367321 - 367
5X-RAY DIFFRACTION5CB84 - 32084 - 320
6X-RAY DIFFRACTION6CB321 - 367321 - 367
7X-RAY DIFFRACTION7AA374 - 410374 - 410
8X-RAY DIFFRACTION8CB374 - 410374 - 410
9X-RAY DIFFRACTION9AA418 - 543418 - 543
10X-RAY DIFFRACTION10CB418 - 543418 - 543
11X-RAY DIFFRACTION11AA544 - 558544 - 558
12X-RAY DIFFRACTION12CB544 - 558544 - 558
13X-RAY DIFFRACTION13AA559 - 746559 - 746
14X-RAY DIFFRACTION14CB559 - 746559 - 746
15X-RAY DIFFRACTION15AA747 - 868747 - 868
16X-RAY DIFFRACTION16CB747 - 868747 - 868
17X-RAY DIFFRACTION17AA869 - 932869 - 932
18X-RAY DIFFRACTION18CB869 - 932869 - 932
19X-RAY DIFFRACTION19AA933 - 1031933 - 1031
20X-RAY DIFFRACTION20CB933 - 1031933 - 1031
21X-RAY DIFFRACTION21AA1032 - 10661032 - 1066
22X-RAY DIFFRACTION22CB1032 - 10661032 - 1066

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