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- PDB-1icq: CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1icq | ||||||
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Title | CRYSTAL STRUCTURE OF 12-OXOPHYTODIENOATE REDUCTASE 1 FROM TOMATO COMPLEXED WITH 9R,13R-OPDA | ||||||
![]() | 12-OXOPHYTODIENOATE REDUCTASE 1 | ||||||
![]() | OXIDOREDUCTASE / beta-alpha-barrel / PROTEIN-FMN-(9R / 13R-OPDA)-complex / FMN-SUBSTRATE-complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Breithaupt, C. / Strassner, J. / Breitinger, U. / Huber, R. / Macheroux, P. / Schaller, A. / Clausen, T. | ||||||
![]() | ![]() 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 |
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Remark 600 | HETEROGEN THE THREE LAST CARBONS OF THE PENTENYL CHAIN OF 9R,13R-OPDA ARE DISORDERED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.6 KB | Display | ![]() |
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PDB format | ![]() | 122.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 31.8 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1icpSC ![]() 1icsC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42443.035 Da / Num. of mol.: 2 / Mutation: R142M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 3, 2000 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 54064 / % possible obs: 83.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1790 / % possible all: 54.6 |
Reflection | *PLUS Num. measured all: 99966 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 54.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb: 1ICP Resolution: 2→20 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37.1 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.198 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.1 Å2 | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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