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- PDB-1q45: 12-0xo-phytodienoate reductase isoform 3 -

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Basic information

Entry
Database: PDB / ID: 1q45
Title12-0xo-phytodienoate reductase isoform 3
Components12-oxophytodienoate-10,11-reductase
KeywordsOXIDOREDUCTASE / Flavoprotein / flavoenzyme / xenobiotic reductase / old yellow enzyme / secondary messenger / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / stamen development / jasmonic acid biosynthetic process / response to ozone / oxylipin biosynthetic process / response to fungus / peroxisome / FMN binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPhillips Jr., G.N. / Johnson, K.A. / Bingman, C.A. / Smith, D.W. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2005
Title: X-ray structure of Arabidopsis At2g06050, 12-oxophytodienoate reductase isoform 3
Authors: Malone, T.E. / Madson, S.E. / Wrobel, R.L. / Jeon, W.B. / Rosenberg, N.S. / Johnson, K.A. / Bingman, C.A. / Smith, D.W. / Phillips Jr., G.N. / Markley, J.L. / Fox, B.G.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 12-oxophytodienoate-10,11-reductase
B: 12-oxophytodienoate-10,11-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3954
Polymers85,4822
Non-polymers9132
Water7,386410
1
A: 12-oxophytodienoate-10,11-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1982
Polymers42,7411
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate-10,11-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1982
Polymers42,7411
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.113, 85.068, 121.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein 12-oxophytodienoate-10,11-reductase / E.C.1.3.1.42 / 12-0xo-phytodienoate reductase isoform 3 / 12-oxophytodienoate reductase / OPR3 / DDE1


Mass: 42741.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g06050 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9FUP0, 12-oxophytodienoate reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.37 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Glycine, MEPEG 5000, triethanolamine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMMES1droppH6.0
3100 mM1dropNaCl
40.3 mMTCEP1drop
58.75-10.0 %mmePEG50001reservoir
60.1 Mtriethanolamine1reservoirpH8.0
70.275-0.35 Mglycine1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2003 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 55478 / Num. obs: 50628 / % possible obs: 90.5 % / Observed criterion σ(I): -3 / Redundancy: 6.09 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 0.39 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 1.11 / Num. unique all: 2384 / Rsym value: 0.687 / % possible all: 43.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24.92 Å / Num. obs: 48056 / % possible obs: 91.3 %
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 43.6 %

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SOMOREmodel building
REFMAC5.1.24refinement
SOMOREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.92 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.88 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23588 2572 5.1 %RANDOM
Rwork0.18635 ---
all0.18884 55478 --
obs0.1888 48056 91.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.896 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 62 410 6106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215832
X-RAY DIFFRACTIONr_bond_other_d0.0030.025201
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9637913
X-RAY DIFFRACTIONr_angle_other_deg0.887312087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7735728
X-RAY DIFFRACTIONr_chiral_restr0.1030.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026564
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021203
X-RAY DIFFRACTIONr_nbd_refined0.2110.21589
X-RAY DIFFRACTIONr_nbd_other0.2590.27337
X-RAY DIFFRACTIONr_nbtor_other0.0930.23688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2461
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.225
X-RAY DIFFRACTIONr_mcbond_it0.921.53622
X-RAY DIFFRACTIONr_mcangle_it1.61525798
X-RAY DIFFRACTIONr_scbond_it2.44332210
X-RAY DIFFRACTIONr_scangle_it3.8364.52115
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 86 -
Rwork0.297 1541 -
obs-2384 44 %
Refinement
*PLUS
Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.64

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