+Open data
-Basic information
Entry | Database: PDB / ID: 2aft | |||||||||
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Title | Formylglycine generating enzyme C336S mutant | |||||||||
Components | Sulfatase modifying factor 1 | |||||||||
Keywords | HYDROLASE ACTIVATOR / PROTEIN BINDING / formylglycine / post-translational modification / endoplasmic reticulum / sulfatase | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Roeser, D. / Rudolph, M.G. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aft.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aft.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 2aft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aft_validation.pdf.gz | 739.3 KB | Display | wwPDB validaton report |
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Full document | 2aft_full_validation.pdf.gz | 739.8 KB | Display | |
Data in XML | 2aft_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 2aft_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/2aft ftp://data.pdbj.org/pub/pdb/validation_reports/af/2aft | HTTPS FTP |
-Related structure data
Related structure data | 2afyC 2aiiC 2aijC 2aikC 1y1iS C: citing same article (ref.) S: Starting model for refinement |
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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 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.) Homo sapiens (human) / Cell (production host): fibrosarcoma cells / Cell line (production host): HT1080 / Production host: Homo sapiens (human) / References: UniProt: Q8NBK3 | ||
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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: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.37 % |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 16, 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: 1.66→30 Å / Num. obs: 34103 / % possible obs: 95.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.97 Å2 / Rsym value: 0.063 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2228 / Rsym value: 0.45 / % possible all: 63.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1y1i Resolution: 1.66→25.17 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.862 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / 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: 19.579 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→25.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.663→1.706 Å / Total num. of bins used: 20
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