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- PDB-1oq9: The Crystal Structure of the Complex between Stearoyl Acyl Carrie... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1oq9 | ||||||
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Title | The Crystal Structure of the Complex between Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean) and Acetate. | ||||||
![]() | Acyl-[acyl-carrier protein] desaturase | ||||||
![]() | OXIDOREDUCTASE / di-iron enzyme / four-helix bundle / fatty acid biosynthesis / electron transfer | ||||||
Function / homology | ![]() stearoyl-[acyl-carrier-protein] 9-desaturase / : / stearoyl-[ACP] desaturase activity / stearoyl-CoA 9-desaturase activity / chloroplast stroma / fatty acid biosynthetic process / defense response / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moche, M. / Shanklin, J. / Ghoshal, A.K. / Lindqvist, Y. | ||||||
![]() | ![]() Title: Azide and Acetate Complexes plus two iron-depleted Crystal Structures of the Di-iron Enzyme delta9 Stearoyl-ACP Desaturase-Implications for Oxygen Activation and Catalytic Intermediates Authors: Moche, M. / Shanklin, J. / Ghoshal, A. / Lindqvist, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.1 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 452 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41703.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22337, stearoyl-[acyl-carrier-protein] 9-desaturase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.15 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 12-15% Peg4000, 80mM Cacodylate, 200mM Magnesium Acetate, 75mM Ammonium Sulphate, 0.2% Octyl glucoside, 20% Glycerol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.4 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. all: 16342 / Num. obs: 16245 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.043 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.283 / % possible all: 98.9 |
Reflection | *PLUS Lowest resolution: 253 Å / Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.283 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.845 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 76.978 Å / Origin y: 27.904 Å / Origin z: 0.375 Å
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Refinement | *PLUS Highest resolution: 2.4 Å / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.453 Å |