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- PDB-8auq: OPR3 Y370F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-o... -

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Basic information

Entry
Database: PDB / ID: 8auq
TitleOPR3 Y370F variant in complex with ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate
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-O8I / DI(HYDROXYETHYL)ETHER / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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

Downloads & links

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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)90,6207
Polymers89,2552
Non-polymers1,3655
Water11,043613
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3634
Polymers44,6271
Non-polymers7363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2573
Polymers44,6271
Non-polymers6302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.311, 92.602, 89.982
Angle α, β, γ (deg.)90.000, 99.235, 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 23 or resid 25...A10 - 23
121(chain 'A' and (resid 10 through 23 or resid 25...A25
131(chain 'A' and (resid 10 through 23 or resid 25...A27 - 70
141(chain 'A' and (resid 10 through 23 or resid 25...A72 - 86
151(chain 'A' and (resid 10 through 23 or resid 25...A88 - 94
161(chain 'A' and (resid 10 through 23 or resid 25...A96 - 128
171(chain 'A' and (resid 10 through 23 or resid 25...A132 - 226
181(chain 'A' and (resid 10 through 23 or resid 25...A228 - 232
191(chain 'A' and (resid 10 through 23 or resid 25...A234 - 239
1101(chain 'A' and (resid 10 through 23 or resid 25...A241 - 253
1111(chain 'A' and (resid 10 through 23 or resid 25...A255 - 267
1121(chain 'A' and (resid 10 through 23 or resid 25...A271 - 280
1131(chain 'A' and (resid 10 through 23 or resid 25...A282 - 285
1141(chain 'A' and (resid 10 through 23 or resid 25...A298 - 328
1151(chain 'A' and (resid 10 through 23 or resid 25...A330 - 362
1161(chain 'A' and (resid 10 through 23 or resid 25...A364 - 365
1171(chain 'A' and (resid 10 through 23 or resid 25...A367 - 384
1181(chain 'A' and (resid 10 through 23 or resid 25...A401
1191(chain 'A' and (resid 10 through 23 or resid 25...A501
2201(chain 'B' and (resid 10 through 23 or resid 25...B10 - 23
2211(chain 'B' and (resid 10 through 23 or resid 25...B25
2221(chain 'B' and (resid 10 through 23 or resid 25...B27 - 70
2231(chain 'B' and (resid 10 through 23 or resid 25...B72 - 86
2241(chain 'B' and (resid 10 through 23 or resid 25...B88 - 94
2251(chain 'B' and (resid 10 through 23 or resid 25...B96 - 128
2261(chain 'B' and (resid 10 through 23 or resid 25...B132 - 226
2271(chain 'B' and (resid 10 through 23 or resid 25...B228 - 232
2281(chain 'B' and (resid 10 through 23 or resid 25...B234 - 239
2291(chain 'B' and (resid 10 through 23 or resid 25...B241 - 253
2301(chain 'B' and (resid 10 through 23 or resid 25...B255 - 267
2311(chain 'B' and (resid 10 through 23 or resid 25...B271 - 280
2321(chain 'B' and (resid 10 through 23 or resid 25...B282 - 285
2331(chain 'B' and (resid 10 through 23 or resid 25...B298 - 328
2341(chain 'B' and (resid 10 through 23 or resid 25...B330 - 362
2351(chain 'B' and (resid 10 through 23 or resid 25...B364 - 365
2361(chain 'B' and (resid 10 through 23 or resid 25...B367 - 384
2371(chain 'B' and (resid 10 through 23 or resid 25...B401
2381(chain 'B' and (resid 10 through 23 or resid 25...B501

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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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O8I / ethyl (2~{Z})-2-hydroxyimino-3-oxidanylidene-pentanoate / ethyl (Z)-2-(hydroxyimino)-3-oxopentanoate


Mass: 173.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM (Tris (base); BICINE) pH 8.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM Sodium oxamate; ...Details: 100 mM (Tris (base); BICINE) pH 8.5; 20 mM Sodium formate; 20 mM Ammonium acetate; 20 mM Sodium citrate tribasic dihydrate; 20 mM Potassium sodium tartrate tetrahydrate; 20 mM Sodium oxamate; 20% v/v Ethylene glycol; 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 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: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.42→32.6 Å / Num. obs: 287567 / % possible obs: 98.12 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.41 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.4
Reflection shellResolution: 1.42→1.475 Å / Num. unique obs: 14447 / CC1/2: 0.767

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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: 1.42→32.6 Å / SU ML: 0.1263 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1856 7314 5.01 %
Rwork0.1598 138690 -
obs0.1611 146004 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.85 Å2
Refinement stepCycle: LAST / Resolution: 1.42→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 93 613 6396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00526133
X-RAY DIFFRACTIONf_angle_d0.82948356
X-RAY DIFFRACTIONf_chiral_restr0.0774900
X-RAY DIFFRACTIONf_plane_restr0.00521098
X-RAY DIFFRACTIONf_dihedral_angle_d21.12342272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.27382480.25434516X-RAY DIFFRACTION96.93
1.44-1.460.27272310.23844616X-RAY DIFFRACTION97.7
1.46-1.470.25132450.23124587X-RAY DIFFRACTION98.03
1.47-1.490.22272380.22294644X-RAY DIFFRACTION97.86
1.49-1.510.23752450.20894553X-RAY DIFFRACTION98.2
1.51-1.530.2242240.20764626X-RAY DIFFRACTION97.98
1.53-1.560.22232450.20164613X-RAY DIFFRACTION98.26
1.56-1.580.19892530.19724606X-RAY DIFFRACTION98.3
1.58-1.60.22182430.18484618X-RAY DIFFRACTION98.18
1.6-1.630.2062530.18544647X-RAY DIFFRACTION98.45
1.63-1.660.19862360.17994604X-RAY DIFFRACTION98.51
1.66-1.690.20342510.17674651X-RAY DIFFRACTION98.77
1.69-1.720.20142310.17084669X-RAY DIFFRACTION99.19
1.72-1.760.20942460.16944668X-RAY DIFFRACTION99.25
1.76-1.790.2052660.17044647X-RAY DIFFRACTION99.35
1.79-1.840.18932490.16754682X-RAY DIFFRACTION99.42
1.84-1.880.21132730.17784661X-RAY DIFFRACTION99.42
1.88-1.930.18442660.16334611X-RAY DIFFRACTION99.41
1.93-1.990.18292230.1624734X-RAY DIFFRACTION99.2
1.99-2.050.19732440.16154695X-RAY DIFFRACTION99.3
2.05-2.130.16222290.1584650X-RAY DIFFRACTION99.03
2.13-2.210.18562480.15844642X-RAY DIFFRACTION98.51
2.21-2.310.19492410.16444588X-RAY DIFFRACTION97.18
2.31-2.430.18772110.1624048X-RAY DIFFRACTION85.61
2.43-2.590.19182640.16134624X-RAY DIFFRACTION98.43
2.59-2.790.17542690.15564662X-RAY DIFFRACTION99.48
2.79-3.070.15522390.14724733X-RAY DIFFRACTION99.26
3.07-3.510.17592320.14274709X-RAY DIFFRACTION99.18
3.51-4.420.15662450.13134706X-RAY DIFFRACTION99.22
4.42-32.60.1892260.15594680X-RAY DIFFRACTION96.59

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