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- PDB-2rcm: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase v... -

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Basic information

Entry
Database: PDB / ID: 2rcm
TitleCrystal Structure of Arabidopsis thaliana Allene Oxide Synthase variant (F137L) (At-AOS(F137L), cytochrome P450 74A) at 1.73 A Resolution
ComponentsCytochrome P450 74A
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 / 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 / FOURIER SYNTHESIS / Resolution: 1.73 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
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 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 1.4Aug 30, 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
B: Cytochrome P450 74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7905
Polymers111,4652
Non-polymers1,3253
Water13,836768
1
A: Cytochrome P450 74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3492
Polymers55,7331
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 74A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4413
Polymers55,7331
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.454, 105.275, 162.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 55732.570 Da / Num. of mol.: 2 / Mutation: F137L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CYP74A, AOS / 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.: 768 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, 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: 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: 1.73→100 Å / Num. all: 114180 / Num. obs: 114180 / % possible obs: 99.3 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.73→1.76 Å / % possible all: 97.1

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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 2PHQ

2phq
PDB Unreleased entry


Resolution: 1.73→88.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.504 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19778 5714 5 %RANDOM
Rwork0.17235 ---
all0.17363 108383 --
obs0.17363 108383 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.73→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7412 0 92 768 8272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3532.0110635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30623.466352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.746151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.221554
X-RAY DIFFRACTIONr_chiral_restr0.0910.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026006
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.23683
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25446
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8751.54854
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36327641
X-RAY DIFFRACTIONr_scbond_it2.30533371
X-RAY DIFFRACTIONr_scangle_it3.6224.52990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 390 -
Rwork0.247 7620 -
obs--95.52 %
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)
10.698-0.0340.24690.5846-0.02280.66430.00720.016-0.04840.0144-0.00750.0210.06530.02690.0003-0.06720.00780.0186-0.10160.0066-0.07432.223631.166631.915
20.8102-0.26890.00560.70360.10370.8175-0.0027-0.01970.00050.07040.017-0.02680.0303-0.0696-0.0142-0.0693-0.0157-0.0144-0.08290.0162-0.087823.740260.03453.3949
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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