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Yorodumi- PDB-3mo4: The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mo4 | ||||||
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Title | The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp. infantis ATCC 15697 | ||||||
Components | Alpha-1,3/4-fucosidase | ||||||
Keywords | HYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | Bifidobacterium longum subsp. infantis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å | ||||||
Authors | Tan, K. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2012 Title: Bifidobacterium longum subsp. infantis ATCC 15697 alpha-fucosidases are active on fucosylated human milk oligosaccharides. Authors: Sela, D.A. / Garrido, D. / Lerno, L. / Wu, S. / Tan, K. / Eom, H.J. / Joachimiak, A. / Lebrilla, C.B. / Mills, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mo4.cif.gz | 373.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mo4.ent.gz | 317.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mo4_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 3mo4_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 3mo4_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | 3mo4_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/3mo4 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mo4 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Experimentally unknown. The molecule is likely monomeric. |
-Components
#1: Protein | Mass: 53747.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria) Strain: ATCC 15697 / Gene: Blon_2336 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B7GNN8 #2: Chemical | ChemComp-TYR / | #3: Chemical | ChemComp-FMT / | #4: 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: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.8M succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 315r / Detector: CCD / Date: Apr 16, 2010 / 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: 1.9→42 Å / Num. all: 84888 / Num. obs: 84888 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4205 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.901→41.934 Å / SU ML: 0.23 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.07 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→41.934 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain B |