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- PDB-9em0: OPR3 wild type in its dimeric form with special L6 conformation -

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Basic information

Entry
Database: PDB / ID: 9em0
TitleOPR3 wild type in its dimeric form with special L6 conformation
Components12-oxophytodienoate reductase 3
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme
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 / 12-oxophytodienoate reductase 3
Similarity search - Component
Biological speciesSolanum lycocarpum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBijelic, A. / Macheroux, P. / Kerschbaumer, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Sci Rep / Year: 2024
Title: Analysis of homodimer formation in 12-oxophytodienoate reductase 3 in solutio and crystallo challenges the physiological role of the dimer.
Authors: Kerschbaumer, B. / Macheroux, P. / Bijelic, A.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: 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

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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)89,9535
Polymers88,8022
Non-polymers1,1513
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-18 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.695, 89.659, 80.148
Angle α, β, γ (deg.)90.000, 104.171, 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

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Components

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


Mass: 44401.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycocarpum (plant) / Gene: OPR3 / Production host: Escherichia coli (E. coli) / 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES/Tris (6.5), 50 mM ammonium sulfate, 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.99→47.46 Å / Num. obs: 102435 / % possible obs: 97.19 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.22 Å2 / CC1/2: 0.96 / Rpim(I) all: 0.23 / Net I/σ(I): 2.47
Reflection shellResolution: 1.99→2.09 Å / Num. unique obs: 10325 / CC1/2: 0.15 / Rpim(I) all: 1.71

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.46 Å / SU ML: 0.3589 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2768 825 2.05 %
Rwork0.249 39430 -
obs0.2496 40255 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5675 0 78 61 5814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025890
X-RAY DIFFRACTIONf_angle_d0.45988029
X-RAY DIFFRACTIONf_chiral_restr0.0399886
X-RAY DIFFRACTIONf_plane_restr0.00391044
X-RAY DIFFRACTIONf_dihedral_angle_d14.54792086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.33861370.31576562X-RAY DIFFRACTION99.96
2.34-2.520.35051380.31216552X-RAY DIFFRACTION99.99
2.52-2.770.30521370.29176553X-RAY DIFFRACTION99.99
2.77-3.170.33291370.27676534X-RAY DIFFRACTION99.94
3.17-40.24471370.22576582X-RAY DIFFRACTION99.9
4-47.460.22781390.20376647X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00882542511-0.528685419735-0.6359968158681.487231075440.4044164448350.4080267964760.09780295742380.212129245171-0.0380869748136-0.29316204538-0.1056210042060.23515347561-0.0440094750479-0.0478723789968-0.04864823454140.211049105543-0.005019566114810.06547166566570.155997327826-0.003044758944410.13296415978810.9702990881-2.6415605678128.0204158081
20.417293493211-0.148460193682-0.1653681712980.2637486766910.01456754634340.376654911428-0.04789725226310.1932639471820.0437469965652-0.127224761693-0.0684755001947-0.2025762125280.00396515753773-0.0182239651485-2.917316133210.3941244982820.03218534309910.1457571127580.0621042092835-0.01882149212380.079031883910125.4556077221-4.9369881446735.3942566769
31.20659546862-0.5070494991230.1541045737660.4589345463870.2708473395040.484612099931-0.06599040718470.03078016657430.2027342391470.006393863379690.0300115138181-0.264135701137-0.03032675617520.0701443225073-0.1451812761140.409376139368-0.005330043542110.11105375190.1387869243170.003811019005950.22240632315427.800070242911.713776222735.8758957509
41.379480549640.04358678205050.2290437628890.389472905124-0.2701103666030.589154125225-0.0888012682091-0.2126205272170.01011789456640.290554238436-0.06207521342240.0333836058159-0.0438669238892-0.02161216299690.06246544585210.4093858510060.007382899570370.1063940258490.175215080542-0.002357940164470.20512131337910.122987142513.238330745939.4755544012
50.1341314267020.1687221232180.0333353579040.3103412709690.1033017317160.0469343873834-0.04474476379150.04358361951640.0717703675122-0.01190246859520.004207873556450.326278358685-0.04935114973480.000635700672129-0.4278948902990.0843477207753-0.02267793976540.04008414961520.1515512701370.02714648125550.3009719859161.82005376086-3.7630557436435.8374246682
60.690919919232-0.00603125498776-0.1952450384940.141857903079-0.4129869913661.98210486145-0.0166879626190.0747146709394-0.0219845152049-0.0365642361931-0.01334047296470.0173062835354-0.06452167035570.02879732648050.09277795351671.021412430290.001073579025310.2635192505150.3187964102890.03117510669160.3148303916287.2035310091210.92522307675.0154141941
70.475560985595-0.0609692070585-0.2529522443770.007712744204280.005116875811490.878932865919-0.04070774993210.257984764074-0.132219755291-0.028275769524-0.04803440159180.09669624126270.518043042162-0.0307681039109-0.2989477077760.9898303240410.01774705534370.273138386380.3741181397980.004026960928990.2883902182815.81132928933-2.9320662253368.5736085322
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 10 through 71 )AA10 - 711 - 62
22chain 'A' and (resid 72 through 196 )AA72 - 19663 - 187
33chain 'A' and (resid 197 through 270 )AA197 - 270188 - 261
44chain 'A' and (resid 271 through 332 )AA271 - 332262 - 323
55chain 'A' and (resid 333 through 385 )AA333 - 385324 - 376
66chain 'B' and (resid 10 through 229 )BD10 - 2291 - 220
77chain 'B' and (resid 230 through 384 )BD230 - 384221 - 373

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