[English] 日本語
Yorodumi- PDB-1n2k: Crystal structure of a covalent intermediate of endogenous human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n2k | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a covalent intermediate of endogenous human arylsulfatase A | |||||||||
Components | ARYLSULFATASE A | |||||||||
Keywords | HYDROLASE / PHOSPHATE ESTERS HYDROLYSIS / LYSOSOMAL ENZYME / MODIFIED FORMYLGLYCINE / INHIBITION / METAL ION | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Chruszcz, M. / Laidler, P. / Monkiewicz, M. / Ortlund, E. / Lebioda, L. / Lewinski, K. | |||||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2003 Title: Crystal structure of a covalent intermediate of endogenous human arylsulfatase A. Authors: Chruszcz, M. / Laidler, P. / Monkiewicz, M. / Ortlund, E. / Lebioda, L. / Lewinski, K. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n2k.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n2k.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 1n2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n2k_validation.pdf.gz | 764.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n2k_full_validation.pdf.gz | 770.6 KB | Display | |
Data in XML | 1n2k_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 1n2k_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2k ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52038.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cellular location: LYSOSOME / Organ: PLACENTA / References: UniProt: P15289, cerebroside-sulfatase |
---|---|
#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: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.01 Å3/Da / Density % sol: 69.1 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: cacodylate, sodium fluoride, PEG8000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 294 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 21542 / Biso Wilson estimate: 36.9 Å2 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 22279 / % possible obs: 97.9 % |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→8 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.87 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / Rfactor Rfree: 0.417 / Rfactor Rwork: 0.36 |