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- PDB-2aii: wild-type Formylglycine generating enzyme reacted with iodoacetamide -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aii | |||||||||
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Title | wild-type Formylglycine generating enzyme reacted with iodoacetamide | |||||||||
![]() | Sulfatase modifying factor 1 | |||||||||
![]() | HYDROLASE ACTIVATOR / PROTEIN BINDING / formylglycine / post-translational modification / endoplasmic reticulum / sulfatase | |||||||||
Function / homology | ![]() The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / oxidoreductase activity / endoplasmic reticulum lumen ...The activation of arylsulfatases / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosphingolipid catabolic process / Glycosphingolipid catabolism / cupric ion binding / post-translational protein modification / oxidoreductase activity / endoplasmic reticulum lumen / endoplasmic reticulum / 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.7 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.3 KB | Display | ![]() |
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Full document | ![]() | 745 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2aftC ![]() 2afyC ![]() 2aijC ![]() 2aikC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32126.676 Da / Num. of mol.: 1 / Fragment: residues 86-371 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 | #4: Chemical | ChemComp-ACM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.75 % |
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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: Jan 28, 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: 1.54→50 Å / Num. obs: 44155 / % possible obs: 98.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.19 Å2 / Rsym value: 0.045 / Net I/σ(I): 41.5 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.229 / % possible all: 85.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Y1E Resolution: 1.54→43.48 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.166 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / 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: 11.798 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→43.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.543→1.583 Å / Total num. of bins used: 20
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