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- PDB-8auo: OPR3 Y370F variant in complex with 2-methoxyethyl (Z)-2-(hydroxyi... -

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Basic information

Entry
Database: PDB / ID: 8auo
TitleOPR3 Y370F variant in complex with 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate
Components12-oxophytodienoate reductase 3
KeywordsOXIDOREDUCTASE / Ene-reductase / oxime / FMN / complex
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / jasmonic acid biosynthetic process / oxylipin biosynthetic process / peroxisome / FMN binding / identical protein binding
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-O8R / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsPolidori, N. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Acs Catalysis / Year: 2023
Title: Mechanistic Insights into the Ene-Reductase-Catalyzed Promiscuous Reduction of Oximes to Amines.
Authors: Breukelaar, W.B. / Polidori, N. / Singh, A. / Daniel, B. / Glueck, S.M. / Gruber, K. / Kroutil, W.
History
DepositionAug 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,5466
Polymers89,2552
Non-polymers1,2914
Water12,052669
1
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2733
Polymers44,6271
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2733
Polymers44,6271
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.174, 92.222, 90.257
Angle α, β, γ (deg.)90.000, 99.253, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 10 through 25 or resid 27...A10 - 25
121(chain 'A' and (resid 10 through 25 or resid 27...A27 - 46
131(chain 'A' and (resid 10 through 25 or resid 27...A49 - 89
141(chain 'A' and (resid 10 through 25 or resid 27...A91 - 94
151(chain 'A' and (resid 10 through 25 or resid 27...A96 - 146
161(chain 'A' and (resid 10 through 25 or resid 27...A149 - 160
171(chain 'A' and (resid 10 through 25 or resid 27...A163 - 210
181(chain 'A' and (resid 10 through 25 or resid 27...A212 - 222
191(chain 'A' and (resid 10 through 25 or resid 27...A224 - 226
1101(chain 'A' and (resid 10 through 25 or resid 27...A228 - 232
1111(chain 'A' and (resid 10 through 25 or resid 27...A234 - 240
1121(chain 'A' and (resid 10 through 25 or resid 27...A245 - 253
1131(chain 'A' and (resid 10 through 25 or resid 27...A255 - 260
1141(chain 'A' and (resid 10 through 25 or resid 27...A263 - 279
1151(chain 'A' and (resid 10 through 25 or resid 27...A281 - 283
1161(chain 'A' and (resid 10 through 25 or resid 27...A297 - 324
1171(chain 'A' and (resid 10 through 25 or resid 27...A326 - 328
1181(chain 'A' and (resid 10 through 25 or resid 27...A330 - 331
1191(chain 'A' and (resid 10 through 25 or resid 27...A334 - 362
1201(chain 'A' and (resid 10 through 25 or resid 27...A364
1211(chain 'A' and (resid 10 through 25 or resid 27...A366 - 383
1221(chain 'A' and (resid 10 through 25 or resid 27...A401
211(chain 'B' and (resid 10 through 25 or resid 27...B10 - 25
221(chain 'B' and (resid 10 through 25 or resid 27...B27 - 46
231(chain 'B' and (resid 10 through 25 or resid 27...B49 - 89
241(chain 'B' and (resid 10 through 25 or resid 27...B91 - 94
251(chain 'B' and (resid 10 through 25 or resid 27...B96 - 146
261(chain 'B' and (resid 10 through 25 or resid 27...B149 - 160
271(chain 'B' and (resid 10 through 25 or resid 27...B163 - 210
281(chain 'B' and (resid 10 through 25 or resid 27...B212 - 222
291(chain 'B' and (resid 10 through 25 or resid 27...B224 - 226
2101(chain 'B' and (resid 10 through 25 or resid 27...B228 - 232
2111(chain 'B' and (resid 10 through 25 or resid 27...B234 - 240
2121(chain 'B' and (resid 10 through 25 or resid 27...B245 - 253
2131(chain 'B' and (resid 10 through 25 or resid 27...B255 - 260
2141(chain 'B' and (resid 10 through 25 or resid 27...B263 - 279
2151(chain 'B' and (resid 10 through 25 or resid 27...B281 - 283
2161(chain 'B' and (resid 10 through 25 or resid 27...B297 - 324
2171(chain 'B' and (resid 10 through 25 or resid 27...B326 - 328
2181(chain 'B' and (resid 10 through 25 or resid 27...B330 - 331
2191(chain 'B' and (resid 10 through 25 or resid 27...B334 - 362
2201(chain 'B' and (resid 10 through 25 or resid 27...B364
2211(chain 'B' and (resid 10 through 25 or resid 27...B366 - 383
2221(chain 'B' and (resid 10 through 25 or resid 27...B401

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Components

#1: Protein 12-oxophytodienoate reductase 3 / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3


Mass: 44627.465 Da / Num. of mol.: 2 / Mutation: Y370F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FEW9, 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-O8R / 2-methoxyethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-butanoate / 2-methoxyethyl (Z)-2-(hydroxyimino)-3-oxobutanoate


Mass: 189.166 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C7H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM (Tris (base); BICINE) pH 8.5; 20 mM 1,6-Hexanediol; 20 mM 1-Butanol 20 mM 1,2-Propanediol; 20 mM 2-Propanol; 20 mM 1,4-Butanediol; 20 mM 1,3-Propanediol; 20% v/v PEG 500* MME; 10 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.58→45.83 Å / Num. obs: 106577 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.05
Reflection shellResolution: 1.58→1.636 Å / Num. unique obs: 10783 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
AutoProcessdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3hgs

3hgs


Resolution: 1.58→45.83 Å / SU ML: 0.1581 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.7989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1835 1120 1.05 %
Rwork0.1669 105447 -
obs0.167 106567 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.36 Å2
Refinement stepCycle: LAST / Resolution: 1.58→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5663 0 88 669 6420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626168
X-RAY DIFFRACTIONf_angle_d0.87258405
X-RAY DIFFRACTIONf_chiral_restr0.0563903
X-RAY DIFFRACTIONf_plane_restr0.00531112
X-RAY DIFFRACTIONf_dihedral_angle_d17.17712305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.650.25941420.227513332X-RAY DIFFRACTION99.62
1.65-1.740.23911410.214713329X-RAY DIFFRACTION99.39
1.74-1.850.22481410.186613235X-RAY DIFFRACTION99.01
1.85-1.990.19651400.171113224X-RAY DIFFRACTION98.72
1.99-2.190.21981390.165613075X-RAY DIFFRACTION97.46
2.19-2.510.17161350.162112753X-RAY DIFFRACTION94.9
2.51-3.160.16211420.166813361X-RAY DIFFRACTION99.29
3.16-45.830.16221400.150413138X-RAY DIFFRACTION96.5

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