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Yorodumi- PDB-1wxy: Crystal structure of adenosine deaminase ligated with a potent in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wxy | ||||||
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Title | Crystal structure of adenosine deaminase ligated with a potent inhibitor | ||||||
Components | Adenosine deaminase | ||||||
Keywords | HYDROLASE / beta barel | ||||||
Function / homology | Function and homology information negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process ...negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process / anchoring junction / T cell activation / lysosome / cell adhesion / external side of plasma membrane / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kinoshita, T. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural Basis of Compound Recognition by Adenosine Deaminase Authors: Kinoshita, T. / Nakanishi, I. / Terasaka, T. / Kuno, M. / Seki, N. / Warizaya, M. / Matsumura, H. / Inoue, T. / Takano, K. / Adachi, H. / Mori, Y. / Fujii, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wxy.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wxy.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 1wxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/1wxy ftp://data.pdbj.org/pub/pdb/validation_reports/wx/1wxy | HTTPS FTP |
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-Related 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: 40341.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: intestine / References: UniProt: P56658, adenosine deaminase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-FRK / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Ammonium sulphate, PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.8266 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 1, 2004 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.15 Å / Num. all: 14524 / Num. obs: 14422 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1744054.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PARMSTD.XPL / Topol file: PROTEIN.TOP |