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- PDB-1ics: CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO -

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Basic information

Entry
Database: PDB / ID: 1ics
TitleCRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO
Components12-OXOPHYTODIENOATE REDUCTASE 1
KeywordsOXIDOREDUCTASE / beta-alpha-barrel
Function / homology
Function and homology information


12-oxophytodienoate reductase / 12-oxophytodienoate reductase activity / oxylipin biosynthetic process / NADPH dehydrogenase activity / fatty acid biosynthetic process / FMN binding / oxidoreductase activity / cytosol
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 1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBreithaupt, C. / Strassner, J. / Breitinger, U. / Huber, R. / Macheroux, P. / Schaller, A. / Clausen, T.
CitationJournal: Structure / Year: 2001
Title: X-ray structure of 12-oxophytodienoate reductase 1 provides structural insight into substrate binding and specificity within the family of OYE.
Authors: Breithaupt, C. / Strassner, J. / Breitinger, U. / Huber, R. / Macheroux, P. / Schaller, A. / Clausen, T.
History
DepositionApr 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 9, 2023Group: 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 1
B: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7994
Polymers84,8862
Non-polymers9132
Water5,044280
1
A: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8992
Polymers42,4431
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8992
Polymers42,4431
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.857, 72.027, 72.357
Angle α, β, γ (deg.)62.92, 85.17, 78.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 12-OXOPHYTODIENOATE REDUCTASE 1 / OPR1


Mass: 42443.035 Da / Num. of mol.: 2 / Mutation: R142M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: OPR1 / Plasmid: PGEX-G / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XG54, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Tris/HCl, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMMOPS-KOH1drop
3100 mMTris-HCl1reservoir
41.45 Mammonium sulfate1reservoir
52 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 3, 2000
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 40681 / % possible obs: 96.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 4 / Num. unique all: 1943 / % possible all: 89.6
Reflection
*PLUS
Num. measured all: 73998
Reflection shell
*PLUS
% possible obs: 89.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: pdb: 1ICP

1icp


Resolution: 2.3→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.237 2034 RANDOM
Rwork0.197 --
obs-40587 -
Displacement parametersBiso mean: 38.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 62 280 5908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.39
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.94
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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