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Yorodumi- PDB-1krm: Crystal structure of bovine adenosine deaminase complexed with 6-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1krm | ||||||
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Title | Crystal structure of bovine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine riboside | ||||||
Components | adenosine deaminase | ||||||
Keywords | HYDROLASE / adenosine deaminase | ||||||
Function / homology | Function and homology information negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / inosine biosynthetic process / 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 / cytoplasmic vesicle lumen / inosine biosynthetic process / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kinoshita, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6-dihydropurine riboside. Authors: Kinoshita, T. / Nishio, N. / Nakanishi, I. / Sato, A. / Fujii, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1krm.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1krm.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 1krm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1krm_validation.pdf.gz | 753.6 KB | Display | wwPDB validaton report |
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Full document | 1krm_full_validation.pdf.gz | 786.1 KB | Display | |
Data in XML | 1krm_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 1krm_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/1krm ftp://data.pdbj.org/pub/pdb/validation_reports/kr/1krm | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40326.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Strain: intestine / References: UniProt: P56658, adenosine deaminase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PRH / |
#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: 2.81 Å3/Da / Density % sol: 56.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: ammonium sulphate, PEG400, MES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Kinoshita, T., (1999) Acta Crystallogr.,Sect., D55, 2031. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 12, 1999 / Details: monochromater |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 16308 / Num. obs: 15982 / % possible obs: 75.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rsym value: 0.117 |
Reflection shell | Resolution: 2.5→2.73 Å / Redundancy: 6.4 % / Rsym value: 0.185 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 16108 / % possible obs: 99.2 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.286 | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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