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Yorodumi- PDB-3ank: Crystal structure of unsaturated glucuronyl hydrolase mutant D175... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ank | |||||||||
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Title | Crystal structure of unsaturated glucuronyl hydrolase mutant D175N from Streptcoccus agalactiae complexed with dGlcA-GalNAc6S | |||||||||
Components | Putative uncharacterized protein gbs1889 | |||||||||
Keywords | HYDROLASE / alpha6/alpha6-barrel | |||||||||
Function / homology | Function and homology information unsaturated chondroitin disaccharide hydrolase / chondroitin hydrolase activity / unsaturated chondroitin disaccharide hydrolase activity / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Streptococcus agalactiae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Nakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural determinants in streptococcal unsaturated glucuronyl hydrolase for recognition of glycosaminoglycan sulfate groups Authors: Nakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ank.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ank.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ank.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/3ank ftp://data.pdbj.org/pub/pdb/validation_reports/an/3ank | HTTPS FTP |
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-Related structure data
Related structure data | 3aniC 3anjC 2zzrS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46640.691 Da / Num. of mol.: 1 / Mutation: D175N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: serogroup III/NEM316 / Gene: gbs1889, Ugl / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 References: UniProt: Q8E372, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||
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#2: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-EDO / #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: 2.09 Å3/Da / Density % sol: 41.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 40% ethylene glycol, 5% PEG3000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 21, 2009 |
Radiation | Monochromator: Fixed exit Si(111) double crystal monochromato Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→20 Å / Num. obs: 25199 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Num. unique all: 2470 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZZR Resolution: 2.02→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.605 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R Free: 0.163 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.738 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.016→2.068 Å / Total num. of bins used: 20
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