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- PDB-1c7t: BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACET... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c7t | |||||||||
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Title | BETA-N-ACETYLHEXOSAMINIDASE MUTANT E540D COMPLEXED WITH DI-N ACETYL-D-GLUCOSAMINE (CHITOBIASE) | |||||||||
![]() | BETA-N-ACETYLHEXOSAMINIDASE![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Prag, G. / Papanikolau, Y. / Tavlas, G. / Vorgias, C.E. / Petratos, K. / Oppenheim, A.B. | |||||||||
![]() | ![]() Title: Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540. Authors: Prag, G. / Papanikolau, Y. / Tavlas, G. / Vorgias, C.E. / Petratos, K. / Oppenheim, A.B. #1: ![]() Title: Cloning of the Gene Coding for Chitobiase of Serratia Marcescens Authors: Kless, H. / Sitrit, Y. / Chet, I. / Oppenheim, A.B. #2: ![]() 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 156.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1c7sSC 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: 95970.906 Da / Num. of mol.: 1 Fragment: MATURE PROTEIN, PERIPLASMATIC TARGETING SEQUENCE RESIDUES 1-27 CLEAVED OFF DURING MATURATION Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH DINAG / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||
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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: 2.45 Å3/Da / Density % sol: 49.72 % | |||||||||||||||||||||||||
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Crystal grow![]() | Method: vapor diffusion, hanging drop / pH: 4.8 Details: CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 ...Details: CO-CRYSTALS WERE GROWN BY THE HANGING-DROP VAPOR DIFFUSION METHOD. RESERVOIR BUFFER CONTAINED 2.3 MOLAR AMMONIUM SULFATE AND 100 MILLIMOLAR CACODYLATE BUFFER PH 4.8. PROTEIN SOLUTION 40 MILLIGRAM PER MILLILITER WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR CONTAINING 10 MILLIMOLAR DI-NAG. CRYSTALS ABOUT 0.5 X 0.2 X 0.2 MILLIMETER IN SIZE WERE FORMED WITHIN 2-3 DAYS., VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1999 / Details: 300 MM IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→10 Å / Num. obs: 71983 / % possible obs: 96.9 % / Biso Wilson estimate: 20.95 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10122.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.217 / % possible all: 94 |
Reflection | *PLUS Highest resolution: 1.85 Å / Num. measured all: 1001880 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.95 Å / % possible obs: 94 % / Rmerge(I) obs: 0.216 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1C7S Resolution: 1.9→10 Å / SU B: 3.63 / SU ML: 0.11 / Cross valid method: R-FREE / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.16
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Displacement parameters | Biso mean: 25.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: 'REFMAC / ARP' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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