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

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Basic information

Entry
Database: PDB / ID: 1icp
TitleCRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH PEG400
Components12-OXOPHYTODIENOATE REDUCTASE 1
KeywordsOXIDOREDUCTASE / beta-alpha-barrel / PROTEIN-FMN-PEG complex
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
Remark 600HETEROGEN THE LIGAND 2PE IS ALSO REFERRED TO AS PEG400.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)86,8559
Polymers84,8862
Non-polymers1,9697
Water8,701483
1
A: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4455
Polymers42,4431
Non-polymers1,0024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 12-OXOPHYTODIENOATE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4104
Polymers42,4431
Non-polymers9673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.391, 71.323, 71.525
Angle α, β, γ (deg.)63.71, 83.85, 77.36
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 490 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Tris/HCl, ammonium sulfate, PEG400, 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: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.033 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 66928 / % possible obs: 91.8 % / Redundancy: 1.7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5356 / % possible all: 88.5
Reflection
*PLUS
Num. measured all: 101396
Reflection shell
*PLUS
% possible obs: 88.5 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb: 1OYA

1oya


Resolution: 1.9→22.9 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3395 -RANDOM
Rwork0.182 ---
all-66805 --
obs-63410 91.8 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 129 483 6250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.92
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 22.9 Å / % reflection Rfree: 5 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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