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Yorodumi- PDB-3wn2: Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wn2 | |||||||||
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Title | Crystal Structure of Streptomyces coelicolor alpha-L-arabinofuranosidase in complex with xylohexaose | |||||||||
Components | Extracellular exo-alpha-L-arabinofuranosidase | |||||||||
Keywords | HYDROLASE / five-bladed beta-propeller / Glycoside Hydrolase | |||||||||
Function / homology | Function and homology information L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | Streptomyces coelicolor (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Fujimoto, Z. / Maehara, T. / Ichinose, H. / Michikawa, M. / Harazono, K. / Kaneko, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal structure and characterization of the glycoside hydrolase family 62 alpha-L-arabinofuranosidase from Streptomyces coelicolor Authors: Maehara, T. / Fujimoto, Z. / Ichinose, H. / Michikawa, M. / Harazono, K. / Kaneko, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wn2.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wn2.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wn2 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wn2 | HTTPS FTP |
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-Related structure data
Related structure data | 3wmyC 3wmzC 3wn0C 3wn1SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 46524.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: abfB, SC7H1.02, SCO5932 / Plasmid: pDNCAex.1 / Production host: Streptomyces lividans (bacteria) / Strain (production host): 1326 References: UniProt: O54161, non-reducing end alpha-L-arabinofuranosidase |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 261 molecules
#3: Chemical | ChemComp-CA / | ||
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#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-TRS / | ||
#6: Chemical | #7: 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: 2.63 Å3/Da / Density % sol: 53.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 20% PEG 3350, 0.2M tri-potassium citrate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2012 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.45 Å / Num. obs: 29718 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 19.361 Å2 / Rsym value: 0.117 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 21.4 % / Mean I/σ(I) obs: 8.5 / Num. unique all: 2910 / Rsym value: 0.512 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WN1 Resolution: 2.1→34.45 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.926 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.255 Å2
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Refine analyze | Luzzati coordinate error obs: 0.078 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→34.45 Å
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Refine LS restraints |
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