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Yorodumi- PDB-1e3c: Crystal structure of an Arylsulfatase A mutant C69S soaked in syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e3c | ||||||||||||
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Title | Crystal structure of an Arylsulfatase A mutant C69S soaked in synthetic substrate | ||||||||||||
Components | Arylsulfatase A | ||||||||||||
Keywords | HYDROLASE / CEREBROSIDE-3-SULFATE HYDROLYSIS / LYSOSOMAL ENZYME / FORMYLGLYCINE | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||||||||
Authors | von Buelow, R. / Schmidt, B. / Dierks, T. / von Figura, K. / Uson, I. | ||||||||||||
Citation | Journal: J. Mol. Biol. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3c.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3c.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 1e3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3c_validation.pdf.gz | 785.2 KB | Display | wwPDB validaton report |
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Full document | 1e3c_full_validation.pdf.gz | 816.2 KB | Display | |
Data in XML | 1e3c_validation.xml.gz | 25 KB | Display | |
Data in CIF | 1e3c_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3c ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3c | HTTPS FTP |
-Related structure data
Related structure data | 1e1zC 1e2sC 1aukS 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: 51943.734 Da / Num. of mol.: 1 / Mutation: C69S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: LYSOSOME / Gene: ARSA / Organ: TESTIS / Cell line (production host): MEF / Production host: Mus musculus (house mouse) / References: UniProt: P15289, cerebroside-sulfatase |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 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: 2.65→40 Å / Num. obs: 24966 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.077 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.65→2.75 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.34 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.364 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AUK Resolution: 2.65→40 Å / SU B: 7.52 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.35 / ESU R Free: 0.261
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Displacement parameters | Biso mean: 36.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |