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Yorodumi- PDB-3anj: Crystal structure of unsaturated glucuronyl hydrolase from Strept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3anj | ||||||
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Title | Crystal structure of unsaturated glucuronyl hydrolase 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: 1.95 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 | 3anj.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3anj.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3anj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/3anj ftp://data.pdbj.org/pub/pdb/validation_reports/an/3anj | HTTPS FTP |
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-Related structure data
Related structure data | 3aniC 3ankC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46641.680 Da / Num. of mol.: 1 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: 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: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% PEG200, 0.1M HEPES, 1% PEG3000, pH 7.0, 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: Dec 11, 2008 |
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: 1.95→50 Å / Num. obs: 28120 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.006 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.29 / Num. unique all: 2595 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZZR Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.582 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R Free: 0.151 / 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: 25.959 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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