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Open data
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Basic information
Entry | Database: PDB / ID: 1e1z | ||||||||||||
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Title | Crystal structure of an Arylsulfatase A mutant C69S | ||||||||||||
![]() | Arylsulfatase A | ||||||||||||
![]() | HYDROLASE / CEREBROSIDE-3-SULFATE HYDROLYSIS / LYSOSOMAL ENZYME / FORMYLGLYCINE | ||||||||||||
Function / homology | ![]() cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / Glycosphingolipid catabolism / lysosomal lumen / lipid metabolic process / azurophil granule lumen / lysosome ...cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / Glycosphingolipid catabolism / lysosomal lumen / lipid metabolic process / azurophil granule lumen / lysosome / endoplasmic reticulum lumen / calcium ion binding / Neutrophil degranulation / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | von Buelow, R. / Schmidt, B. / Dierks, T. / von Figura, K. / Uson, I. | ||||||||||||
![]() | ![]() Title: Crystal structure of an enzyme-substrate complex provides insight into the interaction between human arylsulfatase A and its substrates during catalysis. Authors: von Bulow, R. / Schmidt, B. / Dierks, T. / von Figura, K. / Uson, I. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 82.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 834 KB | Display | ![]() |
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Full document | ![]() | 855.1 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e2sC ![]() 1e3cC ![]() 1aukS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51942.750 Da / Num. of mol.: 1 / Mutation: C69S Source method: isolated from a genetically manipulated source 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-MG / |
#4: Water | ChemComp-HOH / |
Compound details | CHAIN P ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR ...Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION IN HANGING DROPS AT 291 K. SOLUTION CONTAINING 10MG/ML PROTEIN, 10 MM TRIS/HCL (PH 7.4) AND 150 MM NACL WAS MIXED WITH SAME VOLUME OF RESERVOIR SOLUTION, CONTAINING 100 MM NA-ACETATE (PH 5.0 - 5.4) AND 10 - 13 % PEG 6000 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18-22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: Dec 15, 1998 / Details: BENT CRYSTAL |
Radiation | Monochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 33145 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.41 / % possible all: 98.5 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.439 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AUK Resolution: 2.4→30 Å / SU B: 5.42 / SU ML: 0.127 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.21
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Displacement parameters | Biso mean: 39.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |