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- PDB-3cli: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase (... -

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Basic information

Entry
Database: PDB / ID: 3cli
TitleCrystal Structure of Arabidopsis thaliana Allene Oxide Synthase (AOS, cytochrome P450 74A, CYP74A) at 1.80 A Resolution
ComponentsAllene Oxide Synthase
KeywordsLYASE / P450 fold
Function / homology
Function and homology information


oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / plastoglobule / jasmonic acid biosynthetic process / epoxygenase P450 pathway / chloroplast thylakoid / oxylipin biosynthetic process / response to fungus / response to jasmonic acid ...oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / plastoglobule / jasmonic acid biosynthetic process / epoxygenase P450 pathway / chloroplast thylakoid / oxylipin biosynthetic process / response to fungus / response to jasmonic acid / thylakoid / chloroplast envelope / plastid / chloroplast thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / defense response to fungus / chloroplast / monooxygenase activity / defense response / oxygen binding / response to wounding / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Allene oxide synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLee, D.-S. / Nioche, P. / Raman, C.S.
CitationJournal: Nature / Year: 2008
Title: Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes
Authors: Lee, D.-S. / Nioche, P. / Hamberg, M. / Raman, C.S.
History
DepositionMar 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
B: Allene Oxide Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8585
Polymers111,5332
Non-polymers1,3253
Water11,656647
1
A: Allene Oxide Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3832
Polymers55,7671
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Allene Oxide Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4753
Polymers55,7671
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.639, 105.192, 162.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer

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Components

#1: Protein Allene Oxide Synthase / E.C.4.2.1.92 / Cytochrome P450 74A / chloroplast / Hydroperoxide dehydrase


Mass: 55766.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AOS, CYP74A / Plasmid: pcWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q96242, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, Glycerol, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2007
RadiationMonochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 100757 / Num. obs: 100757 / % possible obs: 99.2 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.84 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→88.39 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.194 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 5023 5 %RANDOM
Rwork0.17 ---
all0.171 95613 --
obs0.171 95613 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 92 647 8157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227835
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3722.00910645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14123.446354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4391554
X-RAY DIFFRACTIONr_chiral_restr0.0970.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23691
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2565
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9011.54862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40327641
X-RAY DIFFRACTIONr_scbond_it2.42533385
X-RAY DIFFRACTIONr_scangle_it3.7374.53000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 380 -
Rwork0.259 6861 -
obs--97.27 %
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)
10.6082-0.04560.2260.5997-0.00060.68550.0077-0.012-0.05170.0397-0.00920.03480.07040.02430.0015-0.04920.01170.0187-0.07070.0104-0.05512.244431.219831.9184
20.7196-0.2553-0.05370.70430.12510.79470.004900.01270.05160.0067-0.04470.0117-0.0556-0.0116-0.0629-0.0099-0.0096-0.06360.013-0.0823.80559.95323.3868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA52 - 48625 - 459
2X-RAY DIFFRACTION2BB52 - 48625 - 459

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