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Yorodumi- PDB-7l74: Crystal structure of Beta-hexosyl transferase from Hamamotoa (Spo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l74 | ||||||
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Title | Crystal structure of Beta-hexosyl transferase from Hamamotoa (Sporobolomyces) singularis bound to TRIS | ||||||
Components | Beta-hexosyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / Beta-galactosidase-like enzyme Function and homology information | ||||||
Biological species | Hamamotoa singularis (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Dagher, S.F. / Edwards, B.F.P. / Meilleur, F. / Bruno-Barcena, J.M. | ||||||
Citation | Journal: To Be Published Title: Structure and mutagenic analysis of the Beta-hexosyltransferase from Hamamotoa (Sporobolomyces) singularis Authors: Dagher, S.F. / Edwards, B.F.P. / Meilleur, F. / Bruno-Barcena, J.M. #1: Journal: Microbiology (Reading) / Year: 2016 Title: A novel N-terminal region of the membrane Beta-hexosyltransferase: its role in secretion of soluble protein by Pichia pastoris. Authors: Dagher, S.F. / Bruno-Barcena, J.M. #2: Journal: Appl Environ Microbiol / Year: 2013 Title: Heterologous expression of a bioactive Beta-hexosyltransferase, an enzyme producer of prebiotics, from Sporobolomyces singularis. Authors: Dagher, S.F. / Azcarate-Peril, M.A. / Bruno-Barcena, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l74.cif.gz | 454 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l74.ent.gz | 372.5 KB | Display | PDB format |
PDBx/mmJSON format | 7l74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/7l74 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/7l74 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 54 - 593 / Label seq-ID: 32 - 571
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-Components
#1: Protein | Mass: 64586.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hamamotoa singularis (fungus) / Gene: bglA / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q564N5 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.46 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Well: 30% PEG 4000, 0.1 M HEPES 7.5, 0.2 M CaCl2 Hanging Drop: 1:1 Protein:Well |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | ||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Aug 24, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→29.97 Å / Num. obs: 59376 / % possible obs: 98.4 % / Redundancy: 4.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.076 / Rrim(I) all: 0.159 / Net I/σ(I): 9.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: raptorX structure prediction Resolution: 2.25→29.96 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 13.923 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 95.05 Å2 / Biso mean: 28.069 Å2 / Biso min: 10.11 Å2
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Refinement step | Cycle: final / Resolution: 2.25→29.96 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 18231 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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