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Open data
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Basic information
Entry | Database: PDB / ID: 1c8y | ||||||
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Title | Endo-Beta-N-Acetylglucosaminidase H, D130A Mutant | ||||||
![]() | ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H | ||||||
![]() | HYDROLASE / (BETA/ALPHA)8-BARREL | ||||||
Function / homology | ![]() mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Rao, V. / Cui, T. / Guan, C. / Van Roey, P. | ||||||
![]() | ![]() Title: Mutations of endo-beta-N-acetylglucosaminidase H active site residues Asp130 and Glu132: activities and conformations. Authors: Rao, V. / Cui, T. / Guan, C. / Van Roey, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.7 KB | Display | ![]() |
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Full document | ![]() | 416.4 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c3fC ![]() 1c8xC ![]() 1c90C ![]() 1c91C ![]() 1c92C ![]() 1c93C 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 on special symmetry positions |
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Components
#1: Protein | Mass: 28481.400 Da / Num. of mol.: 1 / Mutation: D130A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04067, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG1000, 100 MM ZN(AC)2, 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 41776 / Num. obs: 13418 / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.1 Å / % possible all: 96.2 |
Reflection | *PLUS % possible obs: 98.8 % / Redundancy: 3.11 % / Num. measured all: 41776 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 96.2 % |
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Processing
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Refinement | Resolution: 2→10 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.209 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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