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- PDB-2g5w: X-ray crystal structure of Arabidopsis thaliana 12-oxophytodienoa... -

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Basic information

Entry
Database: PDB / ID: 2g5w
TitleX-ray crystal structure of Arabidopsis thaliana 12-oxophytodienoate reductase isoform 3 (AtOPR3) in complex with 8-iso prostaglandin A1 and its cofactor, flavin mononucleotide.
Components12-oxophytodienoate reductase 3
KeywordsOXIDOREDUCTASE / At2g06050 / OPR ISOFORM 3 / FLAVOPROTEIN / FLAVOENZYME / XENOBIOTIC REDUCTASE / OLD YELLOW ENZYME / SECONDARY MESSENGER / STRUCTURAL GENOMICS FUNCTIONAL FOLLOW-UP STUDY / PROTEIN STRUCTURE INITIATIVE / PSI / 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
Chem-8PG / FLAVIN MONONUCLEOTIDE / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.576 Å
AuthorsHan, B.W. / Malone, T.E. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Fox, B.G. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of Arabidopsis thaliana 12-oxophytodienoate reductase isoform 3 in complex with 8-iso prostaglandin A(1).
Authors: Han, B.W. / Malone, T.E. / Kim, D.J. / Bingman, C.A. / Kim, H.J. / Fox, B.G. / Phillips, G.N.
History
DepositionFeb 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 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_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

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Assembly

Deposited unit
A: 12-oxophytodienoate reductase 3
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0686
Polymers85,4822
Non-polymers1,5864
Water1,946108
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5343
Polymers42,7411
Non-polymers7932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5343
Polymers42,7411
Non-polymers7932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.702, 86.608, 123.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThere are 2 biological units in the asymmetric unit (chain A and chain B)

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Components

#1: Protein 12-oxophytodienoate reductase 3 / 12-oxophytodienoate- 10 / 11-reductase 3 / OPDA-reductase 3 / Delayed dehiscence 1 / AtOPR3


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: PVP 13 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) PLACI RARE / 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: Chemical ChemComp-8PG / (8S,12S)-15S-HYDROXY-9-OXOPROSTA-10Z,13E-DIEN-1-OIC ACID / 8-ISO PROSTAGLANDIN A1 (8-ISO PGA1)


Mass: 336.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.10 M SODIUM CHLORIDE, 0.0003 M TECP, 0.010 M MES, pH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (8.75-10.0% MEPEG 5000, 0.275-0.350 M GLYCINE, 0. ...Details: PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.10 M SODIUM CHLORIDE, 0.0003 M TECP, 0.010 M MES, pH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (8.75-10.0% MEPEG 5000, 0.275-0.350 M GLYCINE, 0.10 M TRIETHANOLAMINE pH 8.0), vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98244 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2005
Details: PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS
RadiationMonochromator: INDIRECT LIQUID NITROGEN COOLED DOUBLE CRYSTAL MONOCHROMATOR WITH SI-111 CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98244 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 22750 / % possible obs: 82 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.157 / Χ2: 1 / Net I/σ(I): 9.549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.58-2.673.90.3663.42313650.8350
2.67-2.784.30.33615690.86258.2
2.78-2.9150.317800.91564.9
2.91-3.065.50.25919790.97472.3
3.06-3.255.90.23422311.07981.3
3.25-3.56.10.20825371.04492
3.5-3.856.70.18227301.03798.9
3.85-4.4170.15127721.04899.7
4.41-5.567.10.13328111.01399.9
5.56-506.90.09529760.955100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.701data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q45

1q45


Resolution: 2.576→48.834 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.188 / SU B: 12.958 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1125 4.955 %RANDOM
Rwork0.2021 ---
all0.205 ---
obs0.20512 22704 81.884 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 39.822 Å2
Baniso -1Baniso -2Baniso -3
1--3.003 Å20 Å20 Å2
2---4.135 Å20 Å2
3---7.138 Å2
Refinement stepCycle: LAST / Resolution: 2.576→48.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5623 0 110 108 5841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225873
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.9747961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0595725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20623.473262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83915925
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2391540
X-RAY DIFFRACTIONr_chiral_restr0.0630.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024518
X-RAY DIFFRACTIONr_nbd_refined0.1830.22800
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.24
X-RAY DIFFRACTIONr_mcbond_it0.55223706
X-RAY DIFFRACTIONr_mcangle_it1.07145782
X-RAY DIFFRACTIONr_scbond_it1.50362488
X-RAY DIFFRACTIONr_scangle_it2.30182179
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.576-2.6430.403360.299270.294201747.744
2.643-2.7150.378520.32910290.331196854.929
2.715-2.7940.315540.29411080.295190361.061
2.794-2.8790.323810.2511220.255186364.573
2.879-2.9740.303640.23111790.235178969.48
2.974-3.0780.308710.22812450.232176274.688
3.078-3.1940.286670.21813010.221169680.66
3.194-3.3240.298720.20613410.211161587.492
3.324-3.4710.219680.21513980.215157293.257
3.471-3.640.305710.20814000.213150198.001
3.64-3.8370.267740.19313260.197140599.644
3.837-4.0690.271600.18413080.187137399.636
4.069-4.3490.22580.16512190.167128399.532
4.349-4.6960.229550.15711370.16119399.916
4.696-5.1410.228440.15610660.159111199.91
5.141-5.7450.21480.1829570.1831005100
5.745-6.6260.271500.1868580.19908100
6.626-8.0970.198440.1867220.187766100
8.097-11.3780.172350.1475890.148624100
11.378-70.8880.414210.3133470.31737398.66

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