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- PDB-2gin: X-ray structure of the wt allene oxide cyclase 2 from arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 2gin
TitleX-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana
ComponentsAllene oxide cyclase 2
KeywordsISOMERASE / BETA BARREL
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
Allene oxide cyclase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 29, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Allene oxide cyclase 2
B: Allene oxide cyclase 2
C: Allene oxide cyclase 2
D: Allene oxide cyclase 2
E: Allene oxide cyclase 2
F: Allene oxide cyclase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,26513
Polymers125,7596
Non-polymers5067
Water11,890660
1
A: Allene oxide cyclase 2
B: Allene oxide cyclase 2
C: Allene oxide cyclase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0876
Polymers62,8793
Non-polymers2073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-34 kcal/mol
Surface area20600 Å2
MethodPISA
2
D: Allene oxide cyclase 2
E: Allene oxide cyclase 2
F: Allene oxide cyclase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1797
Polymers62,8793
Non-polymers2994
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-35 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.900, 104.200, 86.700
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 4 / Auth seq-ID: 16 - 188 / Label seq-ID: 16 - 188

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Allene oxide cyclase 2 /


Mass: 20959.811 Da / Num. of mol.: 6 / 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 48.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 14% (w/v) PEG 8000, 6%(v/v) tert. Butanol, 100mM MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: May 28, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 107806 / Num. obs: 107806 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 32.115 Å2 / Rsym value: 0.074 / Net I/σ(I): 11.27
Reflection shellResolution: 1.8→2.1 Å / % possible obs: 82.6 % / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.8 / Num. measured obs: 117839 / Num. unique all: 38302 / Num. unique obs: 33731 / Rsym value: 0.22 / % possible all: 93.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.02 Å45.53 Å
Translation2.02 Å45.53 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BRJ

2brj


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.551 / SU ML: 0.108 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 5393 5 %RANDOM
Rwork0.207 ---
all0.209 107806 --
obs-107806 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.769 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.83 Å2
2---0.38 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 32 660 8822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0228431
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.99311461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03651044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32924.833360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.119151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9941518
X-RAY DIFFRACTIONr_chiral_restr0.1250.21254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026450
X-RAY DIFFRACTIONr_nbd_refined0.2030.23497
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2525
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.216
X-RAY DIFFRACTIONr_mcbond_it0.9431.55196
X-RAY DIFFRACTIONr_mcangle_it1.54328400
X-RAY DIFFRACTIONr_scbond_it2.60733307
X-RAY DIFFRACTIONr_scangle_it3.8374.53061
Refine LS restraints NCS

Ens-ID: 1 / Number: 1364 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.430.5
2BMEDIUM POSITIONAL0.380.5
3CMEDIUM POSITIONAL0.420.5
4DMEDIUM POSITIONAL0.590.5
5EMEDIUM POSITIONAL0.380.5
6FMEDIUM POSITIONAL0.340.5
1AMEDIUM THERMAL1.22
2BMEDIUM THERMAL1.782
3CMEDIUM THERMAL1.642
4DMEDIUM THERMAL1.882
5EMEDIUM THERMAL1.352
6FMEDIUM THERMAL1.482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.5123490.4346362804983.377
1.847-1.8970.4753650.427236787196.57
1.897-1.9520.4163390.337252760599.816
1.952-2.0120.3274240.2837054748399.933
2.012-2.0780.2713510.2316827719299.805
2.078-2.1510.2743580.2196624699399.843
2.151-2.2320.2773450.236354670799.881
2.232-2.3230.3213090.2586175648599.985
2.323-2.4270.2313090.2135916622699.984
2.427-2.5450.2472860.2085661594899.983
2.545-2.6830.2692740.2115385566399.929
2.683-2.8450.2522870.25019530899.962
2.845-3.0410.2272510.19747945045100
3.041-3.2850.2122280.17744524680100
3.285-3.5980.2012220.17441224344100
3.598-4.0210.2081810.16637303911100
4.021-4.6420.1791740.13732803454100
4.642-5.6810.1741550.15627912946100
5.681-8.0170.231240.18921612285100
8.017-500.216620.2021218129199.148

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