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- PDB-1rvg: crystal structure of class II fructose-bisphosphate aldolase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rvg | ||||||
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Title | crystal structure of class II fructose-bisphosphate aldolase from Thermus aquaticus in complex with Y | ||||||
![]() | fructose-1,6-bisphosphate aldolase | ||||||
![]() | LYASE / CLASS II ALDOLASE / METAL-DEPDENDENT ALDOLASE | ||||||
Function / homology | ![]() tagatose-bisphosphate aldolase activity / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Izard, T. / Sygusch, J. | ||||||
![]() | ![]() Title: Induced Fit Movements and Metal Cofactor Selectivity of Class II Aldolases: STRUCTURE OF THERMUS AQUATICUS FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE. Authors: Izard, T. / 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 | ![]() | 261.2 KB | Display | ![]() |
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PDB format | ![]() | 210.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.8 KB | Display | ![]() |
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Full document | ![]() | 436.5 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 45.4 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33141.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 995 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/YT3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/YT3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CO / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-YT3 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.05 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 295 K / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.105 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 99328 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.2 Å2 |
Reflection | *PLUS Highest resolution: 2 Å / Redundancy: 9.2 % / Num. measured all: 912165 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 92.9 % / Rmerge(I) obs: 0.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The authors used Sr scattering factors which are virtually identical to those of Yttrium for refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.949 Å2 / ksol: 0.359181 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 40.6 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å |