+Open data
-Basic information
Entry | Database: PDB / ID: 8f9o | ||||||
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Title | Dog sialic acid esterase (SIAE) | ||||||
Components | Sialic acid acetylesterase | ||||||
Keywords | HYDROLASE / sialic acid / sialate o-acetylesterase | ||||||
Function / homology | Sialate O-acetylesterase / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / sialate O-acetylesterase activity / SGNH hydrolase superfamily / Sialate O-acetylesterase domain-containing protein Function and homology information | ||||||
Biological species | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Ide, D. / Gorelik, A. / Illes, K. / Nagar, B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: Dog sialic acid esterase (SIAE) Authors: Ide, D. / Gorelik, A. / Illes, K. / Nagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f9o.cif.gz | 412.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f9o.ent.gz | 282.1 KB | Display | PDB format |
PDBx/mmJSON format | 8f9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f9o_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8f9o_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8f9o_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 8f9o_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/8f9o ftp://data.pdbj.org/pub/pdb/validation_reports/f9/8f9o | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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 / Non-polymers , 2 types, 851 molecules A
#1: Protein | Mass: 56173.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8C0LZX8, sialate O-acetylesterase |
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#7: Water | ChemComp-HOH / |
-Sugars , 5 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: 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 |
#6: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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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: 3.42 Å3/Da / Density % sol: 64.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.01 M tri-sodium citrate, 16% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 413696 / % possible obs: 98 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.11 Å2 / Rrim(I) all: 0.096 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 1.25→1.29 Å / Num. unique obs: 33962 / CC1/2: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→35.85 Å / SU ML: 0.0722 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.2906 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→35.85 Å
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Refine LS restraints |
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LS refinement shell |
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