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Yorodumi- PDB-1kic: Inosine-adenosine-guanosine preferring nucleoside hydrolase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kic | ||||||
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Title | Inosine-adenosine-guanosine preferring nucleoside hydrolase from Trypanosoma vivax: Asp10Ala mutant in complex with inosine | ||||||
Components | inosine-adenosine-guanosine preferring nucleoside hydrolase | ||||||
Keywords | HYDROLASE / Rossmann-fold-like motif | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing N-glycosyl compounds / nucleobase-containing compound metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma vivax (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Versees, W. / Decanniere, K. / Van Holsbeke, E. / Devroede, N. / Steyaert, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kic.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kic.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/1kic ftp://data.pdbj.org/pub/pdb/validation_reports/ki/1kic | HTTPS FTP |
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-Related structure data
Related structure data | 1kieC 1hozS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Trypanosoma vivax (eukaryote) / Plasmid: pQE-30 (Qiagen) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 / References: UniProt: Q9GPQ4, purine nucleosidase #2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-NOS / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.71 % | ||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9326 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2000 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9326 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 76141 / Num. obs: 76141 / % possible obs: 92.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 6.1 / Num. unique all: 11058 / % possible all: 64.32 |
Reflection | *PLUS % possible obs: 92.7 % / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 60.4 % / Rmerge(I) obs: 0.195 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HOZ Resolution: 1.6→50 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: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.61 Å /
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Refinement | *PLUS Rfactor obs: 0.1761 / Rfactor Rfree: 0.1939 / Rfactor Rwork: 0.1761 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.24 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 |