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Yorodumi- PDB-3m6d: The crystal structure of the d307a mutant of glycoside Hydrolase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m6d | ||||||
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Title | The crystal structure of the d307a mutant of glycoside Hydrolase (family 31) from ruminococcus obeum atcc 29174 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | HYDROLASE / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Tan, K. / Tesar, C. / Freeman, L. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Faseb J. / Year: 2010 Title: Novel alpha-glucosidase from human gut microbiome: substrate specificities and their switch. 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 | 3m6d.cif.gz | 267.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m6d.ent.gz | 215.8 KB | Display | PDB format |
PDBx/mmJSON format | 3m6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/3m6d ftp://data.pdbj.org/pub/pdb/validation_reports/m6/3m6d | HTTPS FTP |
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-Related structure data
Related structure data | 3m46C 3mkkC 3n04C 3ffj C: citing same article (ref.) S: Starting model for refinement |
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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: 77405.453 Da / Num. of mol.: 2 / Mutation: D307A 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): PPK1037 / References: UniProt: A5ZY13 |
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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: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M BIS-TRIS, 25% PEG3350, 5MM MALTOSE, 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: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2010 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 29095 / Num. obs: 29095 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1847 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FFJ 3ffj Resolution: 2.9→49.78 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.834 / SU B: 53.165 / SU ML: 0.441 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.548 / 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: 54.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→49.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.897→2.972 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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