[English] 日本語
Yorodumi- PDB-1lg2: CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITH ETHYLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lg2 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITH ETHYLENE GLYCOL | ||||||
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: 2.1 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lg2.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lg2.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lg2_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1lg2_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 1lg2_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 1lg2_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/1lg2 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/1lg2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40784.695 Da / Num. of mol.: 1 / Fragment: residues 22-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q13231 | ||
---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.2 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jul 1, 2001 |
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: 2.1→50 Å / Num. obs: 20542 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 22.184 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.9 / Num. unique all: 1330 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 13.4 Å / Num. obs: 20533 / Redundancy: 3.6 % / Num. measured all: 73055 |
Reflection shell | *PLUS % possible obs: 97 % / Redundancy: 3.2 % / Num. unique obs: 1330 / Num. measured obs: 4290 / Mean I/σ(I) obs: 4.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN CHITOTRIOSIADSE TETRAGONAL CRYSTAL FORM Resolution: 2.1→23.64 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1089189.58 / Data cutoff high rms absF: 1089189.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1673 Å2 / ksol: 0.395364 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→23.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 13.4 Å / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|