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Open data
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Basic information
Entry | Database: PDB / ID: 3vgd | ||||||
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Title | Ctystal structure of glycosyltrehalose trehalohydrolase (D252E) | ||||||
![]() | Malto-oligosyltrehalose trehalohydrolase | ||||||
![]() | HYDROLASE / alpha/beta barrel / trehalose / trehalohydrolase / alpha-amylase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Okazaki, N. / Tamada, T. / Feese, M.D. / Kato, M. / Miura, Y. / Komeda, T. / Kobayashi, K. / Kondo, K. / Kuroki, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.7 KB | Display | ![]() |
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PDB format | ![]() | 203.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 473.8 KB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vgbC ![]() 3vgeC ![]() 3vgfC ![]() 3vggC ![]() 3vghC ![]() 1eh9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 64755.762 Da / Num. of mol.: 1 / Mutation: D252E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q55088, 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase | ||
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#2: Chemical | ChemComp-FLC / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.61 % |
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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: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 23, 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: 2.4→94.18 Å / Num. obs: 40919 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EH9 Resolution: 2.4→61.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1823 / WRfactor Rwork: 0.1468 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.897 / SU B: 9.837 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1981 / SU Rfree: 0.1735 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / 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: 93.59 Å2 / Biso mean: 36.9521 Å2 / Biso min: 15.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→61.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.403→2.465 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.0782 Å / Origin y: 33.6153 Å / Origin z: 22.5317 Å
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