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Yorodumi- PDB-1lq0: CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE AT 2.2 ANGSTROM RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lq0 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE AT 2.2 ANGSTROM RESOLUTION | ||||||
Components | CHITOTRIOSIDASE | ||||||
Keywords | HYDROLASE / CHITINASE / CHITIN / GAUCHER | ||||||
Function / homology | Function and homology information endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fusetti, F. / Rozeboom, H.J. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure of human chitotriosidase. Implications for specific inhibitor design and function of mammalian chitinase-like lectins Authors: Fusetti, F. / Von Moeller, H. / Houston, D. / Rozeboom, H.J. / Dijkstra, B.W. / Boot, R.G. / Aerts, J.M. / Van Aalten, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lq0.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lq0.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lq0 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lq0 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40784.695 Da / Num. of mol.: 1 / Fragment: residues 22-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q13231 |
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#2: 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: 2.51 Å3/Da / Density % sol: 50.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 21843 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2 / Num. unique all: 2169 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: chitinase Resolution: 2.2→41.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1885724.93 / Data cutoff high rms absF: 1885724.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9712 Å2 / ksol: 0.364912 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.5 Å2
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Refine analyze | Luzzati coordinate error free: 0.34 Å / Luzzati sigma a free: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→41.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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