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- PDB-3dsk: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase v... -

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Basic information

Entry
Database: PDB / ID: 3dsk
TitleCrystal Structure of Arabidopsis thaliana Allene Oxide Synthase variant (F137L) (At-AOS(F137L), Cytochrome P450 74A, CYP74A) Complexed with 12R,13S-Vernolic Acid at 1.55 A Resolution
ComponentsCytochrome P450 74A, chloroplast
KeywordsLYASE / P450 fold / 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 / 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 / N-OCTANE / Chem-T25 / Allene oxide synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 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 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)113,49910
Polymers111,4652
Non-polymers2,0348
Water13,475748
1
A: Cytochrome P450 74A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9446
Polymers55,7331
Non-polymers1,2115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 74A, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5554
Polymers55,7331
Non-polymers8233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.612, 105.463, 162.632
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: 55732.570 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, 756 molecules

#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-T25 / (9Z)-11-[(2R,3S)-3-pentyloxiran-2-yl]undec-9-enoic acid / 12R,13S-epoxy-9(Z)-octadecenoic acid


Mass: 296.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O3
#4: Chemical ChemComp-OCT / N-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


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


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
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: 0.9998 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: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. all: 155392 / Num. obs: 155392 / % possible obs: 98.9 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.55→1.58 Å / % possible all: 97.6

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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: 1.55→88.39 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.538 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20633 7791 5 %RANDOM
Rwork0.18227 ---
all0.18347 147287 --
obs0.18347 147287 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.579 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7420 0 141 748 8309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2922.01310844
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18123.557357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.936151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8841554
X-RAY DIFFRACTIONr_chiral_restr0.0850.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23670
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25545
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2564
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.54922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22627780
X-RAY DIFFRACTIONr_scbond_it2.06733448
X-RAY DIFFRACTIONr_scangle_it3.2124.53057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.554→1.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 547 -
Rwork0.307 10115 -
obs--92.51 %
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)
10.5625-0.04630.19280.4674-0.02030.5433-0.0003-0.0097-0.05950.0291-0.00040.03920.0470.02460.0007-0.04110.00580.0193-0.04380.0104-0.05392.406131.275531.9941
20.5837-0.1597-0.01830.57210.12010.59970.01410.00480.01060.008-0.006-0.04270.0099-0.0366-0.0082-0.0462-0.00340.0011-0.03760.0118-0.07323.874560.01923.2772
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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