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Yorodumi- PDB-3vxd: Crystal structure of unsaturated glucuronyl hydrolase mutant D115... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vxd | ||||||
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Title | Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae | ||||||
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 Å | ||||||
Authors | Nakamichi, Y. / Maruyama, Y. / Mikami, B. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: To be Published Title: Crystal structure of unsaturated glucuronyl hydrolase mutant D115N from Streptcoccus agalactiae 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 | 3vxd.cif.gz | 315.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vxd.ent.gz | 258.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxd ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxd | HTTPS FTP |
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-Related structure data
Related structure data | 2zzrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 46640.695 Da / Num. of mol.: 4 / Mutation: D115N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Strain: NEM316 / Gene: gbs1889 / Plasmid: pET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: Q8E372, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | ChemComp-SO4 / #3: 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: 2.24 Å3/Da / Density % sol: 45.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 1.5M ammonium sulphate, 0.1M Tris-HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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 22, 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: 1.87→50 Å / Num. all: 136222 / Num. obs: 133399 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.336 / Num. unique all: 13014 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZZR Resolution: 2→27.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.588 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 24.432 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.48 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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