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Yorodumi- PDB-3ug5: Crystal structure of alpha-L-arabinofuranosidase from Thermotoga ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ug5 | |||||||||
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Title | Crystal structure of alpha-L-arabinofuranosidase from Thermotoga maritima xylose complex | |||||||||
Components | Alpha-L-arabinofuranosidase | |||||||||
Keywords | HYDROLASE / Tim Barrel | |||||||||
Function / homology | Function and homology information L-arabinose metabolic process / alpha-L-arabinofuranosidase activity / polysaccharide catabolic process Similarity search - Function | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Im, D.-H. / Miyazaki, K. / Wakagi, T. / Fushinobu, S. | |||||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2012 Title: Crystal Structures of Glycoside Hydrolase Family 51 alpha-L-Arabinofuranosidase from Thermotoga maritima Authors: Im, D.-H. / Kimura, K.I. / Hayasaka, F. / Tanaka, T. / Noguchi, M. / Kobayashi, A. / Shoda, S. / Miyazaki, K. / Wakagi, T. / Fushinobu, S. #1: Journal: EXTREMOPHILES / Year: 2005 Title: Hyperthermophilic alpha-L: -arabinofuranosidase from Thermotoga maritima MSB8: molecular cloning, gene expression, and characterization of the recombinant protein Authors: Miyazaki, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ug5.cif.gz | 595.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ug5.ent.gz | 491 KB | Display | PDB format |
PDBx/mmJSON format | 3ug5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/3ug5 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/3ug5 | HTTPS FTP |
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-Related structure data
Related structure data | 3ug3C 3ug4C 1pz3S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 4
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-Components
#1: Protein | Mass: 57405.832 Da / Num. of mol.: 6 / Mutation: R4G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0281 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3) References: UniProt: Q9WYB7, non-reducing end alpha-L-arabinofuranosidase #2: Chemical | ChemComp-TRS / #3: Sugar | ChemComp-XYP / #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: 3.73 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1M sodium citrate, 0.1M Tris-HCl, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 10, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 222330 / Num. obs: 221594 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40.6 Å2 / Rsym value: 0.078 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 21880 / Rsym value: 0.38 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PZ3 Resolution: 2.3→29.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.864 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / 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: 34.072 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 3868 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
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