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- PDB-2hib: human formylglycine generating enzyme, C336S mutant, iodide co-cr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hib | |||||||||
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Title | human formylglycine generating enzyme, C336S mutant, iodide co-crystallization | |||||||||
![]() | 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 | ![]() ![]() | |||||||||
![]() | Rudolph, M.G. / Roeser, D. | |||||||||
![]() | ![]() Title: Probing the oxygen-binding site of the human formylglycine-generating enzyme using halide ions. Authors: Roeser, D. / Schmidt, B. / Preusser-Kunze, A. / 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 | ![]() | 77.7 KB | Display | ![]() |
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PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723.6 KB | Display | ![]() |
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Full document | ![]() | 725.6 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hi8C ![]() 2aijS 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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Unit cell |
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Components on special symmetry positions |
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Components
#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: 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-IOD / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, Calcium iodide, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2006 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 72271 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1570 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2aij Resolution: 2→33.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.181 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The close contacts are partial occupancy contacts, where the occupancies of the clashing atoms sum up to one.
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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: 25.822 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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