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- PDB-2hs6: Crystal structure of the E291K mutant of 12-oxophytodienoate redu... -

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Basic information

Entry
Database: PDB / ID: 2hs6
TitleCrystal structure of the E291K mutant of 12-oxophytodienoate reductase 3 (OPR3) from tomato
Components12-oxophytodienoate reductase 3
KeywordsOXIDOREDUCTASE / alpha beta 8 barrel / flavoprotein / jasmonate biosynthesis
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 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 speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBreithaupt, C. / Clausen, T. / Huber, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure of 12-oxophytodienoate reductase 3 from tomato: Self-inhibition by dimerization.
Authors: Breithaupt, C. / Kurzbauer, R. / Lilie, H. / Schaller, A. / Strassner, J. / Huber, R. / Macheroux, P. / Clausen, T.
History
DepositionJul 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE RESIDUE GLU 291 THAT WAS MUTATED TO LYS IS NOT VISIBLE IN THE ELECTRON DENSITY.

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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)90,1066
Polymers88,8022
Non-polymers1,3034
Water7,638424
1
A: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0533
Polymers44,4011
Non-polymers6522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-oxophytodienoate reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0533
Polymers44,4011
Non-polymers6522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.180, 92.240, 90.090
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 12-oxophytodienoate reductase 3 / / 12-oxophytodienoate-10 / 11-reductase 3 / OPDA-reductase 3 / LeOPR3 / OPR3


Mass: 44401.203 Da / Num. of mol.: 2 / Mutation: E291K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FEW9, 12-oxophytodienoate reductase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris HCl, 14% PEG8000, 50 mM Ammonium tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 57790 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.96 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.8 / Num. unique all: 4516 / % possible all: 87.3

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 2922 Random
Rwork0.205 --
obs-57732 -
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 86 424 6128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.31

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