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

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Basic information

Entry
Database: PDB / ID: 3dsi
TitleCrystal Structure of Arabidopsis thaliana Allene Oxide Synthase (AOS, cytochrome P450 74A, CYP74A) Complexed with 13(S)-HOT at 1.60 A resolution
ComponentsCytochrome P450 74A, chloroplast
KeywordsLYASE / P450 / Chloroplast / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Metal-binding / Oxylipin biosynthesis / Transit peptide
Function / homology
Function and homology information


oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / plastoglobule / jasmonic acid biosynthetic process / response to jasmonic acid / chloroplast thylakoid / epoxygenase P450 pathway / oxylipin biosynthetic process / response to fungus ...oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / plastoglobule / jasmonic acid biosynthetic process / response to jasmonic acid / chloroplast thylakoid / epoxygenase P450 pathway / oxylipin biosynthetic process / response to fungus / chloroplast envelope / thylakoid / 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 / N-OCTANE / Chem-T24 / Allene oxide synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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
DepositionJul 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / 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: Cytochrome P450 74A, chloroplast
B: Cytochrome P450 74A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,56510
Polymers111,5332
Non-polymers2,0328
Water14,538807
1
A: Cytochrome P450 74A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9766
Polymers55,7671
Non-polymers1,2095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 74A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5894
Polymers55,7671
Non-polymers8233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.407, 104.851, 162.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450 74A, chloroplast / Allene oxide synthase / Hydroperoxide dehydrase


Mass: 55766.590 Da / Num. of mol.: 2 / Fragment: UNP residues 34-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP74A, AOS, At5g42650, MJB21.2 / Plasmid: pcWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q96242, hydroperoxide dehydratase

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Non-polymers , 5 types, 815 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-T24 / (9Z,11E,13S,15Z)-13-hydroxyoctadeca-9,11,15-trienoic acid


Mass: 294.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O3
#4: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, Glycerol, Tris-HCl, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2007
RadiationMonochromator: double miror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. all: 143678 / Num. obs: 143678 / % possible obs: 99.6 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.6→1.63 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3CLI

3cli


Resolution: 1.6→88.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.384 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18548 7199 5 %RANDOM
Rwork0.16672 ---
all0.16767 136373 --
obs0.16767 136373 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→88.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7426 0 141 807 8374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227987
X-RAY DIFFRACTIONr_angle_refined_deg1.2632.01110851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93523.538359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.088151356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3641554
X-RAY DIFFRACTIONr_chiral_restr0.0830.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026150
X-RAY DIFFRACTIONr_nbd_refined0.2050.23894
X-RAY DIFFRACTIONr_nbtor_refined0.310.25590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2665
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.234
X-RAY DIFFRACTIONr_mcbond_it0.6931.54901
X-RAY DIFFRACTIONr_mcangle_it1.15827780
X-RAY DIFFRACTIONr_scbond_it1.98233456
X-RAY DIFFRACTIONr_scangle_it3.1454.53067
LS refinement shellResolution: 1.595→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 503 -
Rwork0.219 9633 -
obs--95.91 %
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)
10.4676-0.04970.14150.4275-0.01370.5454-0.0061-0.0285-0.05130.029400.03290.05710.02560.0061-0.03450.00920.0171-0.05190.0119-0.03142.518231.131331.9743
20.5313-0.1706-0.08890.51320.09250.60120.00790.01880.0155-0.0006-0.0092-0.046-0.005-0.02810.0013-0.0402-0.00240.0019-0.06070.0103-0.049323.927959.64883.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA51 - 48624 - 459
2X-RAY DIFFRACTION2BB52 - 48625 - 459

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