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Yorodumi- PDB-4wk9: Crystal structure of human chitotriosidase-1 catalytic domain in ... -
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-Basic information
Entry | Database: PDB / ID: 4wk9 | |||||||||
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Title | Crystal structure of human chitotriosidase-1 catalytic domain in complex with chitobiose (0.3mM) at 1.10 A resolution | |||||||||
Components | Chitotriosidase-1 | |||||||||
Keywords | HYDROLASE / CHIT1 / GH18 chitinase / protonation states / hydrolysis / catalytic mechanism | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.102 Å | |||||||||
Authors | Fadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. Authors: Fadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wk9.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wk9.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 4wk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/4wk9 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/4wk9 | HTTPS FTP |
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-Related structure data
Related structure data | 4wjxC 4wkaC 4wkfC 4wkhC 1guvS S: Starting model for refinement C: citing same article (ref.) |
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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: 42224.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13231, chitinase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 25 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate at pH 7.2, 0.3mM 4-methylumbelliferyl triacetylchitotrioside |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2013 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 152249 / % possible obs: 99.51 % / Redundancy: 11.9 % / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.57 / % possible all: 95.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GUV Resolution: 1.102→37.301 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.102→37.301 Å
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Refine LS restraints |
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LS refinement shell |
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