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- PDB-2aik: Formylglycine generating enzyme C336S mutant covalently bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aik | |||||||||
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Title | Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide LCTPSRA | |||||||||
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![]() | HYDROLASE ACTIVATOR / PROTEIN BINDING / formylglycine / post-translational modification / endoplasmic reticulum / sulfatase | |||||||||
Function / homology | ![]() cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / arylsulfatase activity / sulfuric ester hydrolase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism ...cerebroside-sulfatase / cerebroside-sulfatase activity / The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / arylsulfatase activity / sulfuric ester hydrolase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / lysosomal lumen / post-translational protein modification / lipid metabolic process / azurophil granule lumen / oxidoreductase activity / lysosome / endoplasmic reticulum lumen / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Roeser, D. / Rudolph, M.G. | |||||||||
![]() | ![]() Title: A general binding mechanism for all human sulfatases by the formylglycine-generating enzyme Authors: Roeser, D. / Preusser-Kunze, A. / Schmidt, B. / Gasow, K. / Wittmann, J.G. / Dierks, T. / von Figura, K. / Rudolph, M.G. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.6 KB | Display | ![]() |
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PDB format | ![]() | 61.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.3 KB | Display | ![]() |
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Full document | ![]() | 749.3 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aftC ![]() 2afyC ![]() 2aiiC ![]() 2aijC ![]() 1y1eS C: citing same article ( S: Starting model for refinement |
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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
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules XP
#1: Protein | Mass: 32110.613 Da / Num. of mol.: 1 / Fragment: residues 86-371 / Mutation: C336S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein/peptide | Mass: 747.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: P15289 |
#3: 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 |
-Non-polymers , 3 types, 498 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, Calcium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 31093 / % possible obs: 97.8 % / Redundancy: 10.2 % / Rsym value: 0.071 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.373 / % possible all: 87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Y1E Resolution: 1.73→29.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.785 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.391 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→29.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.731→1.776 Å / Total num. of bins used: 20
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