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Yorodumi- PDB-3vgb: Crystal structure of glycosyltrehalose trehalohydrolase (GTHase) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vgb | ||||||
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Title | Crystal structure of glycosyltrehalose trehalohydrolase (GTHase) from Sulfolobus solfataricus KM1 | ||||||
Components | Malto-oligosyltrehalose trehalohydrolase | ||||||
Keywords | HYDROLASE / alpha/beta barrel / trehalose / trehalohydrolase / alpha-amylase | ||||||
Function / homology | Function and homology information 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase / 4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity / trehalose biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å | ||||||
Authors | Okazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Kuroki, R. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Substrate recognition mechanism of a glycosyltrehalose trehalohydrolase from Sulfolobus solfataricus KM1. Authors: Okazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Blaber, M. / Kuroki, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vgb.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vgb.ent.gz | 199.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vgb_validation.pdf.gz | 456.9 KB | Display | wwPDB validaton report |
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Full document | 3vgb_full_validation.pdf.gz | 465.9 KB | Display | |
Data in XML | 3vgb_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 3vgb_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/3vgb ftp://data.pdbj.org/pub/pdb/validation_reports/vg/3vgb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64741.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: treZ / Plasmid: PGUSS2 / Production host: Pichia jadinii (fungus) References: UniProt: Q55088, 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase | ||
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#2: Chemical | ChemComp-FLC / | ||
#3: Chemical | #4: 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: 3.85 Å3/Da / Density % sol: 68.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1M sodium citrate, 0.1M HEPES, 5mM MTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 28, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→94.03 Å / Num. obs: 29375 / % possible obs: 97.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.8 / % possible all: 84.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→67.78 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.1793 / WRfactor Rwork: 0.1441 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8332 / SU B: 26.537 / SU ML: 0.223 / SU R Cruickshank DPI: 0.3983 / SU Rfree: 0.2721 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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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 max: 104.6 Å2 / Biso mean: 44.4984 Å2 / Biso min: 8.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→67.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.652→2.721 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 11.6516 Å / Origin y: 33.3201 Å / Origin z: 22.498 Å
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