+
Open data
-
Basic information
Entry | Database: PDB / ID: 1fgo | ||||||
---|---|---|---|---|---|---|---|
Title | LIPOXYGENASE-1 (SOYBEAN) AT 100K, Q495A MUTANT | ||||||
![]() | SEED LIPOXYGENASE-1 | ||||||
![]() | OXIDOREDUCTASE / DIOXYGENASE / LIPOXYGENASE / METALLOPROTEIN / FATTY ACIDS | ||||||
Function / homology | ![]() linolenate 9R-lipoxygenase activity / linoleate 13S-lipoxygenase / linoleate 13S-lipoxygenase activity / oxylipin biosynthetic process / lipid oxidation / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / fatty acid oxidation / fatty acid biosynthetic process / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tomchick, D.R. / Minor, W. / Holman, T. | ||||||
![]() | ![]() Title: Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1. Authors: Tomchick, D.R. / Phan, P. / Cymborowski, M. / Minor, W. / Holman, T.R. #1: ![]() Title: CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE L-1 AT 1.4 A RESOLUTION Authors: MINOR, W. / STECZKO, J. / STEC, B. / OTWINOWSKI, Z. / BOLIN, J.T. / WALTER, R. / AXELROD, B. #2: ![]() Title: THE STRUCTURE AND FUNCTION OF LIPOXYGENASE Authors: NELSON, M.J. / SEITZ, S.P. #3: ![]() Title: EXPERIMENTAL EVIDENCE FOR EXTENSIVE TUNNELING OF HYDROGEN IN THE LIPOXYGENASE REACTION: IMPLICATIONS FOR ENZYME CATALYSIS Authors: JONSSON, T. / GLICKMAN, M.H. / SUN, S. / KLINMAN, J.P. #4: ![]() Title: NATURE OF THE RATE-LIMITING STEPS IN THE SOYBEAN LIPOXYGENASE-1 REACTION Authors: GLICKMAN, M.H. / KLINMAN, J.P. #5: ![]() Title: THE THREE-DIMENSIONAL STRUCTURE OF AN ARACHIDONIC ACID 15-LIPOXYGENASE Authors: BOYINGTON, J.C. / GAFFNEY, B.J. / AMZEL, L.M. #6: ![]() Title: CRYSTALLOGRAPHIC DETERMINATION OF THE ACTIVE SITE IRON AND ITS LIGANDS IN SOYBEAN LIPOXYGENASE L-1 Authors: MINOR, W. / STECZKO, J. / BOLIN, J.T. / OTWINOWSKI, Z. / AXELROD, B. #7: ![]() Title: CRYSTALLIZATION AND PRELIMINARY X-RAY INVESTIGATION OF LIPOXYGENASE 1 FROM SOYBEANS Authors: STECZKO, J. / MUCHMORE, C.R. / L SMITH, J. / AXELROD, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 195.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 152.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 439.5 KB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 58.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f8nSC ![]() 1fgmC ![]() 1fgqC ![]() 1fgrC ![]() 1fgtC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 94423.078 Da / Num. of mol.: 1 / Mutation: Q495A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG3350, Sodium Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 5.6 / Details: Minor, W., (1996) Biochemistry, 35, 10687. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→20 Å / Num. all: 107797 / Num. obs: 104247 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.67 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Num. unique all: 9793 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 592213 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: IR Starting model: 1F8n Resolution: 1.62→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: anisotropic / Bsol: 49.253 Å2 / ksol: 0.3527 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.727 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.62→1.68 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|