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Yorodumi- PDB-3w5n: Crystal Structure of Streptomyces avermitilis alpha-L-rhamnosidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w5n | ||||||
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Title | Crystal Structure of Streptomyces avermitilis alpha-L-rhamnosidase complexed with L-rhamnose | ||||||
Components | Putative rhamnosidase | ||||||
Keywords | HYDROLASE / fibronectin-type 3 fold / beta-jelly roll / (alpha/alpha)6-barrel / beta-sandwich / Glycoside Hydrolase / L-RHAMNOSIDE | ||||||
Function / homology | Function and homology information alpha-L-rhamnosidase activity / alpha-L-rhamnosidase / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces avermitilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fujimoto, Z. / Jackson, A. / Michikawa, M. / Maehara, T. / Momma, M. / Henrissat, B.F. / Gilbert, H.J. / Kaneko, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The structure of a Streptomyces avermitilis alpha-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement. Authors: Fujimoto, Z. / Jackson, A. / Michikawa, M. / Maehara, T. / Momma, M. / Henrissat, B.F. / Gilbert, H.J. / Kaneko, S. #1: Journal: Biosci.Biotechnol.Biochem. / Year: 2013 Title: Characterization of an alpha-L-Rhamnosidase from Streptomyces avermitilis Authors: Ichinose, H. / Fujimoto, Z. / Kaneko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w5n.cif.gz | 238.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w5n.ent.gz | 184.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w5n_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 3w5n_full_validation.pdf.gz | 457.5 KB | Display | |
Data in XML | 3w5n_validation.xml.gz | 46.1 KB | Display | |
Data in CIF | 3w5n_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/3w5n ftp://data.pdbj.org/pub/pdb/validation_reports/w5/3w5n | HTTPS FTP |
-Related structure data
Related structure data | 3w5mSC 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 6 molecules A
#1: Protein | Mass: 113534.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: SAV_828 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q82PP4, alpha-L-rhamnosidase |
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#3: Sugar | ChemComp-RAM / |
-Non-polymers , 4 types, 1105 molecules
#2: Chemical | ChemComp-CA / | ||||
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#4: Chemical | #5: Chemical | #6: 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: 2.23 Å3/Da / Density % sol: 44.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 10% (w/v) PEG 6000, 5% (v/v) MPD, 0.1M HEPES, pH 6.8, 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-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2009 |
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: 1.8→40.59 Å / Num. obs: 91813 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 14.715 Å2 / Rsym value: 0.084 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 9161 / Rsym value: 0.558 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3W5M Resolution: 1.8→40.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.394 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 19.553 Å2
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Refine analyze | Luzzati coordinate error obs: 0.127 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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