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- PDB-3dfs: Dihydroxyacetone phosphate Schiff base intermediate in D33S mutan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dfs | ||||||
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Title | Dihydroxyacetone phosphate Schiff base intermediate in D33S mutant fructose-1,6-bisphosphate aldolase from rabbit muscle | ||||||
![]() | Fructose-bisphosphate aldolase A | ||||||
![]() | LYASE / aldolase / mutant / iminium / Schiff base / intermediate / covalent / Acetylation / Glycolysis / Phosphoprotein | ||||||
Function / homology | ![]() negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / fructose 1,6-bisphosphate metabolic process / glycolytic process / protein homotetramerization / positive regulation of cell migration / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | St-Jean, M. / Sygusch, J. | ||||||
![]() | ![]() Title: Charge stabilization and entropy reduction of central lysine residues in fructose-bisphosphate aldolase Authors: St-Jean, M. / Blonski, C. / Sygusch, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.1 KB | Display | ![]() |
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PDB format | ![]() | 259.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.3 KB | Display | ![]() |
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Full document | ![]() | 481.5 KB | Display | |
Data in XML | ![]() | 72.7 KB | Display | |
Data in CIF | ![]() | 111.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dfnC ![]() 3dfoC ![]() 3dfpC ![]() 3dfqC ![]() 3dftC ![]() 1zahS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39235.660 Da / Num. of mol.: 4 / Mutation: D33S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-13P / #3: Water | ChemComp-HOH / | Nonpolymer details | 13P LIGAND IS COVALENTLY | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium HEPES, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 109998 / % possible obs: 82.4 % / Redundancy: 3.6 % / Rsym value: 0.065 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4669 / Rsym value: 0.528 / % possible all: 35.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ZAH Resolution: 2.03→44.11 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(I): 1
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Displacement parameters | Biso mean: 20.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→44.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.13 Å
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