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Yorodumi- PDB-3n04: THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (FAMILY 31) FROM R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n04 | |||||||||
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Title | THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 | |||||||||
Components | alpha-glucosidase | |||||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | |||||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Ruminococcus obeum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å | |||||||||
Authors | Tan, K. / Tesar, C. / Freeman, L. / Wilton, R. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
Citation | Journal: Faseb J. / Year: 2010 Title: THE CRYSTAL STRUCTURE OF THE alpha-Glucosidase (FAMILY 31) FROM RUMINOCOCCUS OBEUM ATCC 29174 Authors: Tan, K. / Tesar, C. / Wilton, R. / Keigher, L. / Babnigg, G. / Joachimiak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n04.cif.gz | 563.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n04.ent.gz | 483.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/3n04 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/3n04 | HTTPS FTP |
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-Related structure data
Related structure data | 3m46C 3m6dC 3mkkC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 78715.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus obeum (bacteria) / Strain: ATCC 29174 / Gene: RUMOBE_03919 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pRK1037 / References: UniProt: A5ZY13 #2: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.67 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M BIS-TRIS 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2008 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→44 Å / Num. all: 93200 / Num. obs: 93200 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.02→2.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.28 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.02→43.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.438 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.155 / 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: 23.886 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→43.9 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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