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Open data
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Basic information
Entry | Database: PDB / ID: 1qbb | |||||||||
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Title | BACTERIAL CHITOBIASE COMPLEXED WITH CHITOBIOSE (DINAG) | |||||||||
![]() | CHITOBIASE | |||||||||
![]() | GLYCOSYL HYDROLASE / CHITOBIASE / CHITINOLYSIS / BA8-BARREL | |||||||||
Function / homology | ![]() glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / chitin catabolic process / polysaccharide binding / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / periplasmic space / lysosome / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tews, I. / Perrakis, A. / Oppenheim, A. / Dauter, Z. / Wilson, K.S. / Vorgias, C.E. | |||||||||
![]() | ![]() Title: Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease. Authors: Tews, I. / Perrakis, A. / Oppenheim, A. / Dauter, Z. / Wilson, K.S. / Vorgias, C.E. #1: ![]() Title: N-Acetylglucosaminidase (Chitobiase) from Serratia Marcescens: Gene Sequence, and Protein Production and Purification in Escherichia Coli Authors: Tews, I. / Vincentelli, R. / Vorgias, C.E. #3: ![]() Title: Cloning of the Gene Coding for Chitobiase of Serratia Marcescens Authors: Kless, H. / Sitrit, Y. / Chet, I. / Oppenheim, A.B. #4: ![]() Title: The Crystal Structure of a B-(1,4) Linked Disaccharide A-N,N'Diacetylchitobiose Monohydrate Authors: Mo, F. / Jensen, L.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.8 KB | Display | ![]() |
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PDB format | ![]() | 272 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 746.8 KB | Display | ![]() |
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Full document | ![]() | 767.9 KB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 61.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qbaSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 95923.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH CHITOBIOSE (DINAG) / Source: (gene. exp.) ![]() Description: PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1 - 27 CLEAVED OFF DURING MATURATION Plasmid: PEMBL18 / Production host: ![]() ![]() | ||
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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: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 44.4 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6. DERIVATIZATION CONDITIONS: SOLID ...Details: CRYSTAL WERE GROWN AT ROOM TEMPERATURE FROM HANGING DROPS CONTAINING 62% SATURATED AMMONIUM SULFATE, 1.5% ISOPROPANOL AND 100 MM CACODYLATE, PH 5.6. DERIVATIZATION CONDITIONS: SOLID CHITOBIOSE WAS ADDED TO THE MOTHER LIQUOR TO MAKE UP HIGH CONCENTRATED STOCK SOLUTION, 0.5 TO 1.0 MICRO LITERS OF THE STOCK SOLUTION WERE ADDED TO THE CRYSTALLISATION DROP CONTAINING CRYSTALS. THE CRYSTALS WERE MOUNTED IMMEDIATELY IN GLASS CAPILLARY. EXPOSURE TIME WAS LIMITED TO 10 MINUTES OR LESS. THESE CRYSTALS: 4 MINS 50 SECS. THE CHITOBIOSE WAS SUPPLIED BY SIGMA., vapor diffusion - hanging drop Temp details: room temp | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1994 / Details: SEGMENTED TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→15 Å / Num. obs: 66148 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.02→2.06 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QBA Resolution: 2→15 Å / Cross valid method: R-FREE / σ(F): -4
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Displacement parameters | Biso mean: 14.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |