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- PDB-2dio: Crystal Structure of the Allene Oxide Cyclase 2 with bound inhibi... -

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Basic information

Entry
Database: PDB / ID: 2dio
TitleCrystal Structure of the Allene Oxide Cyclase 2 with bound inhibitor vernolic acid
ComponentsAllene oxide cyclase 2
KeywordsISOMERASE / beta barrel / inhibitor complex
Function / homology
Function and homology information


allene-oxide cyclase / allene-oxide cyclase activity / stromule / jasmonic acid biosynthetic process / chloroplast envelope / chloroplast stroma / chloroplast thylakoid membrane / response to cold / chloroplast / cytosol
Similarity search - Function
AOC barrel-like / Allene oxide cyclase-like / Allene oxide cyclase / Allene oxide cyclase superfamily / Allene oxide cyclase / Allene oxide cyclase/Dirigent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
11-[(2R,3S)-3-PENTYLOXIRAN-2-YL]UNDECANOIC ACID / Allene oxide cyclase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHofmann, E. / Schaller, F. / Zerbe, P.
CitationJournal: Plant Cell / Year: 2006
Title: The Crystal Structure of Arabidopsis thaliana Allene Oxide Cyclase: Insights into the Oxylipin Cyclization Reaction
Authors: Hofmann, E. / Zerbe, P. / Schaller, F.
History
DepositionMar 30, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allene oxide cyclase 2
B: Allene oxide cyclase 2
C: Allene oxide cyclase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7799
Polymers63,0203
Non-polymers7596
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-33 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.500, 99.800, 105.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a trimer chains A,B,C

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Components

#1: Protein Allene oxide cyclase 2 /


Mass: 21006.705 Da / Num. of mol.: 3 / Fragment: Allene oxide cyclase 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT3G25770 / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9LS02, allene-oxide cyclase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EOD / 11-[(2R,3S)-3-PENTYLOXIRAN-2-YL]UNDECANOIC ACID / (+-)-CIS-12,13-EPOXY-9(Z)-OCTADECANOIC ACID / LEUKOTOXIN B / (+-)-VERNOLIC ACID


Mass: 298.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10% PEG3350, 200mM NaCl, 100mM phosphate citrate, pH 4.2, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODECU K-ALPHA11.54
2
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 8, 2004 / Details: mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MONTEL MIRRORSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→38 Å / Num. all: 70876 / Num. obs: 70876 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.165 Å2 / Rsym value: 0.079 / Net I/σ(I): 15.2
Reflection shellResolution: 1.7→1.8 Å / % possible obs: 89.4 % / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Num. measured obs: 44194 / Num. unique all: 10561 / Num. unique obs: 10519 / Rsym value: 0.345 / % possible all: 89.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2BRJ

2brj


Resolution: 1.7→38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.336 / SU ML: 0.076 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3583 5.1 %RANDOM
Rwork0.197 ---
all0.199 70876 --
obs0.199 70876 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.916 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 51 368 4511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224289
X-RAY DIFFRACTIONr_angle_refined_deg1.78425819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87124.833180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27515701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.037159
X-RAY DIFFRACTIONr_chiral_restr0.2340.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023249
X-RAY DIFFRACTIONr_nbd_refined0.210.21982
X-RAY DIFFRACTIONr_nbtor_refined0.310.22916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.218
X-RAY DIFFRACTIONr_mcbond_it1.1251.52690
X-RAY DIFFRACTIONr_mcangle_it1.69324227
X-RAY DIFFRACTIONr_scbond_it2.93931826
X-RAY DIFFRACTIONr_scangle_it4.1344.51583
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 245 -
Rwork0.297 4688 -
obs-4933 89.32 %

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