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- PDB-1kie: Inosine-adenosine-guanosine preferring nucleoside hydrolase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kie | ||||||
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Title | Inosine-adenosine-guanosine preferring nucleoside hydrolase from Trypanosoma vivax: Asp10Ala mutant in complex with 3-deaza-adenosine | ||||||
![]() | inosine-adenosine-guanosine preferring nucleoside hydrolase | ||||||
![]() | HYDROLASE / Rossmann-fold-like motif | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing N-glycosyl compounds / nucleobase-containing compound metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Versees, W. / Decanniere, K. / Van Holsbeke, E. / Devroede, N. / Steyaert, J. | ||||||
![]() | ![]() Title: Enzyme-substrate interactions in the purine-specific nucleoside hydrolase from Trypanosoma vivax. Authors: Versees, W. / Decanniere, K. / Van Holsbeke, E. / Devroede, N. / Steyaert, 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 | ![]() | 152.3 KB | Display | ![]() |
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PDB format | ![]() | 116.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1006.7 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kicSC 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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Unit cell |
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Components
#1: Protein | Mass: 37674.973 Da / Num. of mol.: 2 / Mutation: D10A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.61 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM tris, 1.6 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
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: Aug 20, 2001 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 36763 / Num. obs: 36763 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3372 / % possible all: 95.2 |
Reflection | *PLUS Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.349 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS TO INOSINE COMPLEX, PDB ENTRY 1KIC Starting model: PDB ENTRY 1KIC Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.1564 / Rfactor Rfree: 0.2153 / Rfactor Rwork: 0.1564 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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