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- PDB-3dbm: Crystal Structure of Allene oxide synthase -

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Basic information

Entry
Database: PDB / ID: 3dbm
TitleCrystal Structure of Allene oxide synthase
ComponentsCytochrome P450 74A2
KeywordsLYASE / crystal structure HEM HODE AOS / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Metal-binding / Oxylipin biosynthesis
Function / homology
Function and homology information


hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / oxylipin biosynthetic process / sterol metabolic process / chloroplast envelope / chloroplast thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, E-class, group IV / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / (9E,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid / Allene oxide synthase CYP74A2
Similarity search - Component
Biological speciesParthenium argentatum (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, L. / Wang, X.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase.
Authors: Li, L. / Chang, Z. / Pan, Z. / Fu, Z.Q. / Wang, X.
History
DepositionJun 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / 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

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Assembly

Deposited unit
A: Cytochrome P450 74A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4463
Polymers53,5331
Non-polymers9132
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.300, 128.300, 160.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Cytochrome P450 74A2 / Allene oxide synthase / Rubber particle protein / RPP


Mass: 53532.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parthenium argentatum (plant) / Gene: CYP74A2, RPP30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q40778, hydroperoxide dehydratase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-HO2 / (9E,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid


Mass: 296.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H32O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M (NH4)H2PO4, 50%MPD, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 20900 / Num. obs: 20482 / % possible obs: 98 % / Redundancy: 98 % / Biso Wilson estimate: 11 Å2 / Rsym value: 0.113 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 96 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1978 / Rsym value: 0.333 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAM

3dam


Resolution: 2.6→49.25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 41885.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2009 9.8 %RANDOM
Rwork0.219 ---
obs0.219 20475 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.5769 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 64 147 3953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 311 9.4 %
Rwork0.305 2984 -
obs-2984 96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hem.par&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4sub.par&_1_TOPOLOGY_INFILE_4

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