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Yorodumi- PDB-2hi8: human formylglycine generating enzyme, C336S mutant, bromide co-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hi8 | |||||||||
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Title | human formylglycine generating enzyme, C336S mutant, bromide co-crystallization | |||||||||
Components |
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Keywords | HYDROLASE ACTIVATOR / PROTEIN BINDING / formylglycin generation / post-translational modification / endoplasmic reticulum / sulfatase | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Rudolph, M.G. / Roeser, D. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hi8.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hi8.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hi8 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hi8 | HTTPS FTP |
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-Related structure data
Related structure data | 2hibC 2afyS S: Starting model for refinement C: citing same article (ref.) |
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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
-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.) Homo sapiens (human) / Cell (production host): fibrosarcoma cells / Production host: Homo sapiens (human) / References: UniProt: Q8NBK3 |
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#2: Protein/peptide | Mass: 563.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P15289*PLUS |
#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 , 4 types, 454 molecules
#4: Chemical | ChemComp-BR / #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.84 % |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 30, 2006 |
Radiation | Monochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. obs: 35818 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.075 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Num. unique all: 2823 / Rsym value: 0.396 / % possible all: 78.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2afy Resolution: 1.64→27.2 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.768 / SU ML: 0.06 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.091 / 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: 12.435 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→27.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.682 Å / Total num. of bins used: 20
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